!date
Mon Mar 14 16:36:33 PDT 2016
%%bash
system_profiler SPSoftwareDataType
Software:
System Software Overview:
System Version: OS X 10.9.5 (13F34)
Kernel Version: Darwin 13.4.0
Boot Volume: Hummingbird
Boot Mode: Normal
Computer Name: hummingbird
User Name: Sam (Sam)
Secure Virtual Memory: Enabled
Time since boot: 115 days 1:27
%%bash
ls /Volumes/nightingales/O_lurida/F15FTSUSAT0768_OYSzenG/
1HL_10A_1.fq.gz 1HL_10A_2.fq.gz 1HL_11A_1.fq.gz 1HL_11A_2.fq.gz 1HL_12A_1.fq.gz 1HL_12A_2.fq.gz 1HL_13A_1.fq.gz 1HL_13A_2.fq.gz 1HL_14A_1.fq.gz 1HL_14A_2.fq.gz 1HL_15A_1.fq.gz 1HL_15A_2.fq.gz 1HL_16A_1.fq.gz 1HL_16A_2.fq.gz 1HL_17A_1.fq.gz 1HL_17A_2.fq.gz 1HL_19A_1.fq.gz 1HL_19A_2.fq.gz 1HL_1A_1.fq.gz 1HL_1A_2.fq.gz 1HL_20A_1.fq.gz 1HL_20A_2.fq.gz 1HL_21A_1.fq.gz 1HL_21A_2.fq.gz 1HL_22A_1.fq.gz 1HL_22A_2.fq.gz 1HL_23A_1.fq.gz 1HL_23A_2.fq.gz 1HL_24A_1.fq.gz 1HL_24A_2.fq.gz 1HL_25A_1.fq.gz 1HL_25A_2.fq.gz 1HL_26A_1.fq.gz 1HL_26A_2.fq.gz 1HL_27A_1.fq.gz 1HL_27A_2.fq.gz 1HL_28A_1.fq.gz 1HL_28A_2.fq.gz 1HL_29A_1.fq.gz 1HL_29A_2.fq.gz 1HL_2A_1.fq.gz 1HL_2A_2.fq.gz 1HL_31A_1.fq.gz 1HL_31A_2.fq.gz 1HL_33A_1.fq.gz 1HL_33A_2.fq.gz 1HL_34A_1.fq.gz 1HL_34A_2.fq.gz 1HL_35A_1.fq.gz 1HL_35A_2.fq.gz 1HL_3A_1.fq.gz 1HL_3A_2.fq.gz 1HL_4A_1.fq.gz 1HL_4A_2.fq.gz 1HL_5A_1.fq.gz 1HL_5A_2.fq.gz 1HL_6A_1.fq.gz 1HL_6A_2.fq.gz 1HL_7A_1.fq.gz 1HL_7A_2.fq.gz 1HL_8A_1.fq.gz 1HL_8A_2.fq.gz 1HL_9A_1.fq.gz 1HL_9A_2.fq.gz 1NF_10A_1.fq.gz 1NF_10A_2.fq.gz 1NF_11A_1.fq.gz 1NF_11A_2.fq.gz 1NF_12A_1.fq.gz 1NF_12A_2.fq.gz 1NF_13A_1.fq.gz 1NF_13A_2.fq.gz 1NF_14A_1.fq.gz 1NF_14A_2.fq.gz 1NF_15A_1.fq.gz 1NF_15A_2.fq.gz 1NF_16A_1.fq.gz 1NF_16A_2.fq.gz 1NF_17A_1.fq.gz 1NF_17A_2.fq.gz 1NF_18A_1.fq.gz 1NF_18A_2.fq.gz 1NF_19A_1.fq.gz 1NF_19A_2.fq.gz 1NF_1A_1.fq.gz 1NF_1A_2.fq.gz 1NF_20A_1.fq.gz 1NF_20A_2.fq.gz 1NF_21A_1.fq.gz 1NF_21A_2.fq.gz 1NF_22A_1.fq.gz 1NF_22A_2.fq.gz 1NF_23A_1.fq.gz 1NF_23A_2.fq.gz 1NF_24A_1.fq.gz 1NF_24A_2.fq.gz 1NF_25A_1.fq.gz 1NF_25A_2.fq.gz 1NF_26A_1.fq.gz 1NF_26A_2.fq.gz 1NF_27A_1.fq.gz 1NF_27A_2.fq.gz 1NF_28A_1.fq.gz 1NF_28A_2.fq.gz 1NF_29A_1.fq.gz 1NF_29A_2.fq.gz 1NF_2A_1.fq.gz 1NF_2A_2.fq.gz 1NF_30A_1.fq.gz 1NF_30A_2.fq.gz 1NF_31A_1.fq.gz 1NF_31A_2.fq.gz 1NF_32A_1.fq.gz 1NF_32A_2.fq.gz 1NF_33A_1.fq.gz 1NF_33A_2.fq.gz 1NF_4A_1.fq.gz 1NF_4A_2.fq.gz 1NF_5A_1.fq.gz 1NF_5A_2.fq.gz 1NF_6A_1.fq.gz 1NF_6A_2.fq.gz 1NF_7A_1.fq.gz 1NF_7A_2.fq.gz 1NF_8A_1.fq.gz 1NF_8A_2.fq.gz 1NF_9A_1.fq.gz 1NF_9A_2.fq.gz 1SN_10A_1.fq.gz 1SN_10A_2.fq.gz 1SN_11A_1.fq.gz 1SN_11A_2.fq.gz 1SN_12A_1.fq.gz 1SN_12A_2.fq.gz 1SN_13A_1.fq.gz 1SN_13A_2.fq.gz 1SN_14A_1.fq.gz 1SN_14A_2.fq.gz 1SN_15A_1.fq.gz 1SN_15A_2.fq.gz 1SN_16A_1.fq.gz 1SN_16A_2.fq.gz 1SN_17A_1.fq.gz 1SN_17A_2.fq.gz 1SN_18A_1.fq.gz 1SN_18A_2.fq.gz 1SN_19A_1.fq.gz 1SN_19A_2.fq.gz 1SN_1A_1.fq.gz 1SN_1A_2.fq.gz 1SN_20A_1.fq.gz 1SN_20A_2.fq.gz 1SN_21A_1.fq.gz 1SN_21A_2.fq.gz 1SN_22A_1.fq.gz 1SN_22A_2.fq.gz 1SN_23A_1.fq.gz 1SN_23A_2.fq.gz 1SN_24A_1.fq.gz 1SN_24A_2.fq.gz 1SN_25A_1.fq.gz 1SN_25A_2.fq.gz 1SN_26A_1.fq.gz 1SN_26A_2.fq.gz 1SN_27A_1.fq.gz 1SN_27A_2.fq.gz 1SN_28A_1.fq.gz 1SN_28A_2.fq.gz 1SN_29A_1.fq.gz 1SN_29A_2.fq.gz 1SN_2A_1.fq.gz 1SN_2A_2.fq.gz 1SN_30A_1.fq.gz 1SN_30A_2.fq.gz 1SN_31A_1.fq.gz 1SN_31A_2.fq.gz 1SN_32A_1.fq.gz 1SN_32A_2.fq.gz 1SN_3A_1.fq.gz 1SN_3A_2.fq.gz 1SN_4A_1.fq.gz 1SN_4A_2.fq.gz 1SN_5A_1.fq.gz 1SN_5A_2.fq.gz 1SN_6A_1.fq.gz 1SN_6A_2.fq.gz 1SN_7A_1.fq.gz 1SN_7A_2.fq.gz 1SN_8A_1.fq.gz 1SN_8A_2.fq.gz 1SN_9A_1.fq.gz 1SN_9A_2.fq.gz UnKnow_1.fq.gz UnKnow_2.fq.gz Upload.tar.gz md5.check md5.txt
%%bash
ls -1 /Volumes/nightingales/O_lurida/F15FTSUSAT0768_OYSzenG/*.fq.gz | wc -l
194
%%bash
#For loop generates a md5 checksum has value for each file
#and appends the output to the checksums.md5 file.
time for file in /Volumes/nightingales/O_lurida/F15FTSUSAT0768_OYSzenG/*.fq.gz
do
md5 "$file" >> /Volumes/nightingales/O_lurida/F15FTSUSAT0768_OYSzenG/checksums.md5
done
real 14m6.296s user 1m33.226s sys 0m27.272s
%%bash
#Initializes variable.
totalreads=0
#For loop counts the lines in each file and divides them by four. This is performed because
#Illumina sequencing files are composed of four lines per read.
#A running total of the total number of reads is generated [totalreads=$((readcount+totalreads))]
#and is printed after the for loop completes.
time for file in /Volumes/nightingales/O_lurida/F15FTSUSAT0768_OYSzenG/*.fq.gz
do linecount=`gunzip -c "$file" | wc -l`
readcount=$((linecount/4))
totalreads=$((readcount+totalreads))
done
echo $totalreads
557596520
real 31m30.449s user 16m21.149s sys 1m54.328s
%%bash
#For loop counts the lines in each file and divides them by four. This is performed because
#Illumina sequencing files are composed of four lines per read.
#Format the output (printf) to print the filename, followed by a tab, followed by the readcount.
#The command "tee -a" is used to both print the output to the screen and append the output to the readme.md file.
time for file in /Volumes/nightingales/O_lurida/F15FTSUSAT0768_OYSzenG/*.fq.gz
do linecount=`gunzip -c "$file" | wc -l`
readcount=$(($linecount/4))
printf "%s\t%s\n\n" "${file##*/}" "$readcount" | tee -a /Volumes/nightingales/O_lurida/F15FTSUSAT0768_OYSzenG/readme.md
done
1HL_10A_1.fq.gz 3186565 1HL_10A_2.fq.gz 3186565 1HL_11A_1.fq.gz 3568503 1HL_11A_2.fq.gz 3568503 1HL_12A_1.fq.gz 2524813 1HL_12A_2.fq.gz 2524813 1HL_13A_1.fq.gz 2676425 1HL_13A_2.fq.gz 2676425 1HL_14A_1.fq.gz 2015611 1HL_14A_2.fq.gz 2015611 1HL_15A_1.fq.gz 2196324 1HL_15A_2.fq.gz 2196324 1HL_16A_1.fq.gz 2333158 1HL_16A_2.fq.gz 2333158 1HL_17A_1.fq.gz 3653761 1HL_17A_2.fq.gz 3653761 1HL_19A_1.fq.gz 3617984 1HL_19A_2.fq.gz 3617984 1HL_1A_1.fq.gz 2260430 1HL_1A_2.fq.gz 2260430 1HL_20A_1.fq.gz 2908938 1HL_20A_2.fq.gz 2908938 1HL_21A_1.fq.gz 2591845 1HL_21A_2.fq.gz 2591845 1HL_22A_1.fq.gz 2074229 1HL_22A_2.fq.gz 2074229 1HL_23A_1.fq.gz 3609794 1HL_23A_2.fq.gz 3609794 1HL_24A_1.fq.gz 2721808 1HL_24A_2.fq.gz 2721808 1HL_25A_1.fq.gz 2957874 1HL_25A_2.fq.gz 2957874 1HL_26A_1.fq.gz 3142369 1HL_26A_2.fq.gz 3142369 1HL_27A_1.fq.gz 3199649 1HL_27A_2.fq.gz 3199649 1HL_28A_1.fq.gz 3770238 1HL_28A_2.fq.gz 3770238 1HL_29A_1.fq.gz 3071205 1HL_29A_2.fq.gz 3071205 1HL_2A_1.fq.gz 2758150 1HL_2A_2.fq.gz 2758150 1HL_31A_1.fq.gz 2453753 1HL_31A_2.fq.gz 2453753 1HL_33A_1.fq.gz 2708943 1HL_33A_2.fq.gz 2708943 1HL_34A_1.fq.gz 2899019 1HL_34A_2.fq.gz 2899019 1HL_35A_1.fq.gz 2630313 1HL_35A_2.fq.gz 2630313 1HL_3A_1.fq.gz 2211401 1HL_3A_2.fq.gz 2211401 1HL_4A_1.fq.gz 2571031 1HL_4A_2.fq.gz 2571031 1HL_5A_1.fq.gz 1980666 1HL_5A_2.fq.gz 1980666 1HL_6A_1.fq.gz 2070051 1HL_6A_2.fq.gz 2070051 1HL_7A_1.fq.gz 2793544 1HL_7A_2.fq.gz 2793544 1HL_8A_1.fq.gz 2544013 1HL_8A_2.fq.gz 2544013 1HL_9A_1.fq.gz 2832945 1HL_9A_2.fq.gz 2832945 1NF_10A_1.fq.gz 2149301 1NF_10A_2.fq.gz 2149301 1NF_11A_1.fq.gz 2266647 1NF_11A_2.fq.gz 2266647 1NF_12A_1.fq.gz 2179923 1NF_12A_2.fq.gz 2179923 1NF_13A_1.fq.gz 3890118 1NF_13A_2.fq.gz 3890118 1NF_14A_1.fq.gz 2719198 1NF_14A_2.fq.gz 2719198 1NF_15A_1.fq.gz 2554324 1NF_15A_2.fq.gz 2554324 1NF_16A_1.fq.gz 2682948 1NF_16A_2.fq.gz 2682948 1NF_17A_1.fq.gz 3119328 1NF_17A_2.fq.gz 3119328 1NF_18A_1.fq.gz 1750070 1NF_18A_2.fq.gz 1750070 1NF_19A_1.fq.gz 2036640 1NF_19A_2.fq.gz 2036640 1NF_1A_1.fq.gz 1355760 1NF_1A_2.fq.gz 1355760 1NF_20A_1.fq.gz 2457026 1NF_20A_2.fq.gz 2457026 1NF_21A_1.fq.gz 3046937 1NF_21A_2.fq.gz 3046937 1NF_22A_1.fq.gz 2895176 1NF_22A_2.fq.gz 2895176 1NF_23A_1.fq.gz 3206742 1NF_23A_2.fq.gz 3206742 1NF_24A_1.fq.gz 3038626 1NF_24A_2.fq.gz 3038626 1NF_25A_1.fq.gz 2203229 1NF_25A_2.fq.gz 2203229 1NF_26A_1.fq.gz 2934794 1NF_26A_2.fq.gz 2934794 1NF_27A_1.fq.gz 2272652 1NF_27A_2.fq.gz 2272652 1NF_28A_1.fq.gz 2344763 1NF_28A_2.fq.gz 2344763 1NF_29A_1.fq.gz 3829981 1NF_29A_2.fq.gz 3829981 1NF_2A_1.fq.gz 3452931 1NF_2A_2.fq.gz 3452931 1NF_30A_1.fq.gz 2701047 1NF_30A_2.fq.gz 2701047 1NF_31A_1.fq.gz 3561574 1NF_31A_2.fq.gz 3561574 1NF_32A_1.fq.gz 3477986 1NF_32A_2.fq.gz 3477986 1NF_33A_1.fq.gz 2602951 1NF_33A_2.fq.gz 2602951 1NF_4A_1.fq.gz 3582899 1NF_4A_2.fq.gz 3582899 1NF_5A_1.fq.gz 2765984 1NF_5A_2.fq.gz 2765984 1NF_6A_1.fq.gz 2423888 1NF_6A_2.fq.gz 2423888 1NF_7A_1.fq.gz 2590507 1NF_7A_2.fq.gz 2590507 1NF_8A_1.fq.gz 2772580 1NF_8A_2.fq.gz 2772580 1NF_9A_1.fq.gz 3380498 1NF_9A_2.fq.gz 3380498 1SN_10A_1.fq.gz 2558667 1SN_10A_2.fq.gz 2558667 1SN_11A_1.fq.gz 2583992 1SN_11A_2.fq.gz 2583992 1SN_12A_1.fq.gz 3423902 1SN_12A_2.fq.gz 3423902 1SN_13A_1.fq.gz 2956991 1SN_13A_2.fq.gz 2956991 1SN_14A_1.fq.gz 3544290 1SN_14A_2.fq.gz 3544290 1SN_15A_1.fq.gz 2506325 1SN_15A_2.fq.gz 2506325 1SN_16A_1.fq.gz 2616966 1SN_16A_2.fq.gz 2616966 1SN_17A_1.fq.gz 2983401 1SN_17A_2.fq.gz 2983401 1SN_18A_1.fq.gz 3248512 1SN_18A_2.fq.gz 3248512 1SN_19A_1.fq.gz 3036463 1SN_19A_2.fq.gz 3036463 1SN_1A_1.fq.gz 3040537 1SN_1A_2.fq.gz 3040537 1SN_20A_1.fq.gz 2155177 1SN_20A_2.fq.gz 2155177 1SN_21A_1.fq.gz 3540618 1SN_21A_2.fq.gz 3540618 1SN_22A_1.fq.gz 3060365 1SN_22A_2.fq.gz 3060365 1SN_23A_1.fq.gz 3696257 1SN_23A_2.fq.gz 3696257 1SN_24A_1.fq.gz 1885265 1SN_24A_2.fq.gz 1885265 1SN_25A_1.fq.gz 3037089 1SN_25A_2.fq.gz 3037089 1SN_26A_1.fq.gz 2758873 1SN_26A_2.fq.gz 2758873 1SN_27A_1.fq.gz 2607809 1SN_27A_2.fq.gz 2607809 1SN_28A_1.fq.gz 2841587 1SN_28A_2.fq.gz 2841587 1SN_29A_1.fq.gz 2257274 1SN_29A_2.fq.gz 2257274 1SN_2A_1.fq.gz 3080107 1SN_2A_2.fq.gz 3080107 1SN_30A_1.fq.gz 3840203 1SN_30A_2.fq.gz 3840203 1SN_31A_1.fq.gz 3353715 1SN_31A_2.fq.gz 3353715 1SN_32A_1.fq.gz 2552635 1SN_32A_2.fq.gz 2552635 1SN_3A_1.fq.gz 2442489 1SN_3A_2.fq.gz 2442489 1SN_4A_1.fq.gz 3294871 1SN_4A_2.fq.gz 3294871 1SN_5A_1.fq.gz 3000852 1SN_5A_2.fq.gz 3000852 1SN_6A_1.fq.gz 3354310 1SN_6A_2.fq.gz 3354310 1SN_7A_1.fq.gz 2964594 1SN_7A_2.fq.gz 2964594 1SN_8A_1.fq.gz 3269810 1SN_8A_2.fq.gz 3269810 1SN_9A_1.fq.gz 3177205 1SN_9A_2.fq.gz 3177205 UnKnow_1.fq.gz 7344729 UnKnow_2.fq.gz 7344729
real 35m56.559s user 16m21.347s sys 1m55.365s