Job ID = 5720326 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,463,817 reads read : 48,927,634 reads written : 24,463,817 reads 0-length : 24,463,817 rm: cannot remove ‘[DSE]RR*’: 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: 00:08:08 24463817 reads; of these: 24463817 (100.00%) were unpaired; of these: 851423 (3.48%) aligned 0 times 16184785 (66.16%) aligned exactly 1 time 7427609 (30.36%) aligned >1 times 96.52% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 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_sort_core] merging from 12 files... [bam_rmdupse_core] 7932528 / 23612394 = 0.3359 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, 15 Apr 2020 23:45:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.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, 15 Apr 2020 23:45:37: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:45:37: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:45:43: 1000000 INFO @ Wed, 15 Apr 2020 23:45:49: 2000000 INFO @ Wed, 15 Apr 2020 23:45:56: 3000000 INFO @ Wed, 15 Apr 2020 23:46:02: 4000000 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, 15 Apr 2020 23:46:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.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, 15 Apr 2020 23:46:07: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:46:07: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:46:08: 5000000 INFO @ Wed, 15 Apr 2020 23:46:15: 1000000 INFO @ Wed, 15 Apr 2020 23:46:16: 6000000 INFO @ Wed, 15 Apr 2020 23:46:22: 2000000 INFO @ Wed, 15 Apr 2020 23:46:23: 7000000 INFO @ Wed, 15 Apr 2020 23:46:29: 3000000 INFO @ Wed, 15 Apr 2020 23:46:30: 8000000 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, 15 Apr 2020 23:46:36: 4000000 INFO @ Wed, 15 Apr 2020 23:46:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.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, 15 Apr 2020 23:46:37: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:46:37: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:46:37: 9000000 INFO @ Wed, 15 Apr 2020 23:46:44: 5000000 INFO @ Wed, 15 Apr 2020 23:46:45: 1000000 INFO @ Wed, 15 Apr 2020 23:46:45: 10000000 INFO @ Wed, 15 Apr 2020 23:46:51: 6000000 INFO @ Wed, 15 Apr 2020 23:46:52: 11000000 INFO @ Wed, 15 Apr 2020 23:46:52: 2000000 INFO @ Wed, 15 Apr 2020 23:46:59: 7000000 INFO @ Wed, 15 Apr 2020 23:46:59: 12000000 INFO @ Wed, 15 Apr 2020 23:47:00: 3000000 INFO @ Wed, 15 Apr 2020 23:47:06: 8000000 INFO @ Wed, 15 Apr 2020 23:47:07: 13000000 INFO @ Wed, 15 Apr 2020 23:47:07: 4000000 INFO @ Wed, 15 Apr 2020 23:47:13: 9000000 INFO @ Wed, 15 Apr 2020 23:47:14: 14000000 INFO @ Wed, 15 Apr 2020 23:47:14: 5000000 INFO @ Wed, 15 Apr 2020 23:47:20: 10000000 INFO @ Wed, 15 Apr 2020 23:47:21: 15000000 INFO @ Wed, 15 Apr 2020 23:47:21: 6000000 INFO @ Wed, 15 Apr 2020 23:47:26: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:47:26: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:47:26: #1 total tags in treatment: 15679866 INFO @ Wed, 15 Apr 2020 23:47:26: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:47:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:47:26: #1 tags after filtering in treatment: 15679866 INFO @ Wed, 15 Apr 2020 23:47:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:47:26: #1 finished! INFO @ Wed, 15 Apr 2020 23:47:26: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:47:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:47:27: #2 number of paired peaks: 1448 INFO @ Wed, 15 Apr 2020 23:47:27: start model_add_line... INFO @ Wed, 15 Apr 2020 23:47:27: 11000000 INFO @ Wed, 15 Apr 2020 23:47:27: start X-correlation... INFO @ Wed, 15 Apr 2020 23:47:27: end of X-cor INFO @ Wed, 15 Apr 2020 23:47:27: #2 finished! INFO @ Wed, 15 Apr 2020 23:47:27: #2 predicted fragment length is 181 bps INFO @ Wed, 15 Apr 2020 23:47:27: #2 alternative fragment length(s) may be 181 bps INFO @ Wed, 15 Apr 2020 23:47:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.05_model.r INFO @ Wed, 15 Apr 2020 23:47:27: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:47:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:47:28: 7000000 INFO @ Wed, 15 Apr 2020 23:47:34: 12000000 INFO @ Wed, 15 Apr 2020 23:47:35: 8000000 INFO @ Wed, 15 Apr 2020 23:47:41: 13000000 INFO @ Wed, 15 Apr 2020 23:47:42: 9000000 INFO @ Wed, 15 Apr 2020 23:47:48: 14000000 INFO @ Wed, 15 Apr 2020 23:47:49: 10000000 INFO @ Wed, 15 Apr 2020 23:47:55: 15000000 INFO @ Wed, 15 Apr 2020 23:47:56: 11000000 INFO @ Wed, 15 Apr 2020 23:48:00: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:48:00: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:48:00: #1 total tags in treatment: 15679866 INFO @ Wed, 15 Apr 2020 23:48:00: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:48:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:48:00: #1 tags after filtering in treatment: 15679866 INFO @ Wed, 15 Apr 2020 23:48:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:48:00: #1 finished! INFO @ Wed, 15 Apr 2020 23:48:00: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:48:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:48:01: #2 number of paired peaks: 1448 INFO @ Wed, 15 Apr 2020 23:48:01: start model_add_line... INFO @ Wed, 15 Apr 2020 23:48:01: start X-correlation... INFO @ Wed, 15 Apr 2020 23:48:01: end of X-cor INFO @ Wed, 15 Apr 2020 23:48:01: #2 finished! INFO @ Wed, 15 Apr 2020 23:48:01: #2 predicted fragment length is 181 bps INFO @ Wed, 15 Apr 2020 23:48:01: #2 alternative fragment length(s) may be 181 bps INFO @ Wed, 15 Apr 2020 23:48:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.10_model.r INFO @ Wed, 15 Apr 2020 23:48:01: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:48:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:48:03: 12000000 INFO @ Wed, 15 Apr 2020 23:48:04: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:48:10: 13000000 INFO @ Wed, 15 Apr 2020 23:48:16: 14000000 INFO @ Wed, 15 Apr 2020 23:48:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:48:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:48:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.05_summits.bed INFO @ Wed, 15 Apr 2020 23:48:21: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (13027 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:48:23: 15000000 INFO @ Wed, 15 Apr 2020 23:48:27: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:48:27: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:48:27: #1 total tags in treatment: 15679866 INFO @ Wed, 15 Apr 2020 23:48:27: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:48:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:48:27: #1 tags after filtering in treatment: 15679866 INFO @ Wed, 15 Apr 2020 23:48:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:48:27: #1 finished! INFO @ Wed, 15 Apr 2020 23:48:27: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:48:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:48:28: #2 number of paired peaks: 1448 INFO @ Wed, 15 Apr 2020 23:48:28: start model_add_line... INFO @ Wed, 15 Apr 2020 23:48:28: start X-correlation... INFO @ Wed, 15 Apr 2020 23:48:28: end of X-cor INFO @ Wed, 15 Apr 2020 23:48:28: #2 finished! INFO @ Wed, 15 Apr 2020 23:48:28: #2 predicted fragment length is 181 bps INFO @ Wed, 15 Apr 2020 23:48:28: #2 alternative fragment length(s) may be 181 bps INFO @ Wed, 15 Apr 2020 23:48:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.20_model.r INFO @ Wed, 15 Apr 2020 23:48:28: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:48:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:48:38: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:48:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:48:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:48:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.10_summits.bed INFO @ Wed, 15 Apr 2020 23:48:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7374 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:49:04: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 15 Apr 2020 23:49:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:49:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:49:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971795/SRX7971795.20_summits.bed INFO @ Wed, 15 Apr 2020 23:49:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3348 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。