Job ID = 6161895 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 454,553 reads read : 454,553 reads written : 454,553 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR1938675.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:03 454553 reads; of these: 454553 (100.00%) were unpaired; of these: 219572 (48.31%) aligned 0 times 170320 (37.47%) aligned exactly 1 time 64661 (14.23%) aligned >1 times 51.69% overall alignment rate Time searching: 00:00:03 Overall time: 00:00:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 20122 / 234981 = 0.0856 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 27 May 2020 12:50:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 27 May 2020 12:50:19: #1 read tag files... INFO @ Wed, 27 May 2020 12:50:19: #1 read treatment tags... INFO @ Wed, 27 May 2020 12:50:21: #1 tag size is determined as 50 bps INFO @ Wed, 27 May 2020 12:50:21: #1 tag size = 50 INFO @ Wed, 27 May 2020 12:50:21: #1 total tags in treatment: 214859 INFO @ Wed, 27 May 2020 12:50:21: #1 user defined the maximum tags... INFO @ Wed, 27 May 2020 12:50:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 27 May 2020 12:50:21: #1 tags after filtering in treatment: 214858 INFO @ Wed, 27 May 2020 12:50:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 27 May 2020 12:50:21: #1 finished! INFO @ Wed, 27 May 2020 12:50:21: #2 Build Peak Model... INFO @ Wed, 27 May 2020 12:50:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 27 May 2020 12:50:21: #2 number of paired peaks: 2161 INFO @ Wed, 27 May 2020 12:50:21: start model_add_line... INFO @ Wed, 27 May 2020 12:50:21: start X-correlation... INFO @ Wed, 27 May 2020 12:50:21: end of X-cor INFO @ Wed, 27 May 2020 12:50:21: #2 finished! INFO @ Wed, 27 May 2020 12:50:21: #2 predicted fragment length is 200 bps INFO @ Wed, 27 May 2020 12:50:21: #2 alternative fragment length(s) may be 200 bps INFO @ Wed, 27 May 2020 12:50:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.05_model.r INFO @ Wed, 27 May 2020 12:50:21: #3 Call peaks... INFO @ Wed, 27 May 2020 12:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 27 May 2020 12:50:21: #3 Call peaks for each chromosome... INFO @ Wed, 27 May 2020 12:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.05_peaks.xls INFO @ Wed, 27 May 2020 12:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.05_peaks.narrowPeak INFO @ Wed, 27 May 2020 12:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.05_summits.bed INFO @ Wed, 27 May 2020 12:50:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (102 records, 4 fields): 6 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 27 May 2020 12:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 27 May 2020 12:50:49: #1 read tag files... INFO @ Wed, 27 May 2020 12:50:49: #1 read treatment tags... INFO @ Wed, 27 May 2020 12:50:50: #1 tag size is determined as 50 bps INFO @ Wed, 27 May 2020 12:50:50: #1 tag size = 50 INFO @ Wed, 27 May 2020 12:50:50: #1 total tags in treatment: 214859 INFO @ Wed, 27 May 2020 12:50:50: #1 user defined the maximum tags... INFO @ Wed, 27 May 2020 12:50:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 27 May 2020 12:50:50: #1 tags after filtering in treatment: 214858 INFO @ Wed, 27 May 2020 12:50:50: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 27 May 2020 12:50:50: #1 finished! INFO @ Wed, 27 May 2020 12:50:50: #2 Build Peak Model... INFO @ Wed, 27 May 2020 12:50:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 27 May 2020 12:50:50: #2 number of paired peaks: 2161 INFO @ Wed, 27 May 2020 12:50:50: start model_add_line... INFO @ Wed, 27 May 2020 12:50:50: start X-correlation... INFO @ Wed, 27 May 2020 12:50:50: end of X-cor INFO @ Wed, 27 May 2020 12:50:50: #2 finished! INFO @ Wed, 27 May 2020 12:50:50: #2 predicted fragment length is 200 bps INFO @ Wed, 27 May 2020 12:50:50: #2 alternative fragment length(s) may be 200 bps INFO @ Wed, 27 May 2020 12:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.10_model.r INFO @ Wed, 27 May 2020 12:50:50: #3 Call peaks... INFO @ Wed, 27 May 2020 12:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 27 May 2020 12:50:50: #3 Call peaks for each chromosome... INFO @ Wed, 27 May 2020 12:50:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.10_peaks.xls INFO @ Wed, 27 May 2020 12:50:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.10_peaks.narrowPeak INFO @ Wed, 27 May 2020 12:50:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.10_summits.bed INFO @ Wed, 27 May 2020 12:50:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (47 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 27 May 2020 12:51:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 27 May 2020 12:51:19: #1 read tag files... INFO @ Wed, 27 May 2020 12:51:19: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 27 May 2020 12:51:20: #1 tag size is determined as 50 bps INFO @ Wed, 27 May 2020 12:51:20: #1 tag size = 50 INFO @ Wed, 27 May 2020 12:51:20: #1 total tags in treatment: 214859 INFO @ Wed, 27 May 2020 12:51:20: #1 user defined the maximum tags... INFO @ Wed, 27 May 2020 12:51:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 27 May 2020 12:51:20: #1 tags after filtering in treatment: 214858 INFO @ Wed, 27 May 2020 12:51:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 27 May 2020 12:51:20: #1 finished! INFO @ Wed, 27 May 2020 12:51:20: #2 Build Peak Model... INFO @ Wed, 27 May 2020 12:51:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 27 May 2020 12:51:20: #2 number of paired peaks: 2161 INFO @ Wed, 27 May 2020 12:51:20: start model_add_line... INFO @ Wed, 27 May 2020 12:51:20: start X-correlation... INFO @ Wed, 27 May 2020 12:51:20: end of X-cor INFO @ Wed, 27 May 2020 12:51:20: #2 finished! INFO @ Wed, 27 May 2020 12:51:20: #2 predicted fragment length is 200 bps INFO @ Wed, 27 May 2020 12:51:20: #2 alternative fragment length(s) may be 200 bps INFO @ Wed, 27 May 2020 12:51:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.20_model.r INFO @ Wed, 27 May 2020 12:51:20: #3 Call peaks... INFO @ Wed, 27 May 2020 12:51:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 27 May 2020 12:51:20: #3 Call peaks for each chromosome... INFO @ Wed, 27 May 2020 12:51:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.20_peaks.xls INFO @ Wed, 27 May 2020 12:51:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.20_peaks.narrowPeak INFO @ Wed, 27 May 2020 12:51:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999208/ERX1999208.20_summits.bed INFO @ Wed, 27 May 2020 12:51:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (16 records, 4 fields): 1 millis CompletedMACS2peakCalling