Job ID = 5720239 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,401,878 reads read : 24,401,878 reads written : 24,401,878 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: 00:04:50 24401878 reads; of these: 24401878 (100.00%) were unpaired; of these: 2369993 (9.71%) aligned 0 times 18719354 (76.71%) aligned exactly 1 time 3312531 (13.57%) aligned >1 times 90.29% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 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] 9163787 / 22031885 = 0.4159 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 22:55:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.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 22:55:34: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:55:34: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:55:40: 1000000 INFO @ Wed, 15 Apr 2020 22:55:47: 2000000 INFO @ Wed, 15 Apr 2020 22:55:54: 3000000 INFO @ Wed, 15 Apr 2020 22:56:00: 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 22:56:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.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 22:56:03: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:56:03: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:56:07: 5000000 INFO @ Wed, 15 Apr 2020 22:56:10: 1000000 INFO @ Wed, 15 Apr 2020 22:56:13: 6000000 INFO @ Wed, 15 Apr 2020 22:56:16: 2000000 INFO @ Wed, 15 Apr 2020 22:56:20: 7000000 INFO @ Wed, 15 Apr 2020 22:56:23: 3000000 INFO @ Wed, 15 Apr 2020 22:56:26: 8000000 INFO @ Wed, 15 Apr 2020 22:56:30: 4000000 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 22:56:33: 9000000 INFO @ Wed, 15 Apr 2020 22:56:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.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 22:56:33: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:56:33: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:56:36: 5000000 INFO @ Wed, 15 Apr 2020 22:56:40: 10000000 INFO @ Wed, 15 Apr 2020 22:56:40: 1000000 INFO @ Wed, 15 Apr 2020 22:56:44: 6000000 INFO @ Wed, 15 Apr 2020 22:56:47: 11000000 INFO @ Wed, 15 Apr 2020 22:56:47: 2000000 INFO @ Wed, 15 Apr 2020 22:56:51: 7000000 INFO @ Wed, 15 Apr 2020 22:56:54: 12000000 INFO @ Wed, 15 Apr 2020 22:56:55: 3000000 INFO @ Wed, 15 Apr 2020 22:56:58: 8000000 INFO @ Wed, 15 Apr 2020 22:57:00: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:57:00: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:57:00: #1 total tags in treatment: 12868098 INFO @ Wed, 15 Apr 2020 22:57:00: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:57:00: #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 22:57:01: #1 tags after filtering in treatment: 12868098 INFO @ Wed, 15 Apr 2020 22:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:57:01: #1 finished! INFO @ Wed, 15 Apr 2020 22:57:01: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:57:02: 4000000 INFO @ Wed, 15 Apr 2020 22:57:02: #2 number of paired peaks: 2487 INFO @ Wed, 15 Apr 2020 22:57:02: start model_add_line... INFO @ Wed, 15 Apr 2020 22:57:02: start X-correlation... INFO @ Wed, 15 Apr 2020 22:57:02: end of X-cor INFO @ Wed, 15 Apr 2020 22:57:02: #2 finished! INFO @ Wed, 15 Apr 2020 22:57:02: #2 predicted fragment length is 168 bps INFO @ Wed, 15 Apr 2020 22:57:02: #2 alternative fragment length(s) may be 168 bps INFO @ Wed, 15 Apr 2020 22:57:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.05_model.r INFO @ Wed, 15 Apr 2020 22:57:02: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:57:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:57:05: 9000000 INFO @ Wed, 15 Apr 2020 22:57:08: 5000000 INFO @ Wed, 15 Apr 2020 22:57:12: 10000000 INFO @ Wed, 15 Apr 2020 22:57:15: 6000000 INFO @ Wed, 15 Apr 2020 22:57:18: 11000000 INFO @ Wed, 15 Apr 2020 22:57:22: 7000000 INFO @ Wed, 15 Apr 2020 22:57:25: 12000000 INFO @ Wed, 15 Apr 2020 22:57:29: 8000000 INFO @ Wed, 15 Apr 2020 22:57:31: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:57:31: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:57:31: #1 total tags in treatment: 12868098 INFO @ Wed, 15 Apr 2020 22:57:31: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:57:31: #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 22:57:32: #1 tags after filtering in treatment: 12868098 INFO @ Wed, 15 Apr 2020 22:57:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:57:32: #1 finished! INFO @ Wed, 15 Apr 2020 22:57:32: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:57:33: #2 number of paired peaks: 2487 INFO @ Wed, 15 Apr 2020 22:57:33: start model_add_line... INFO @ Wed, 15 Apr 2020 22:57:33: start X-correlation... INFO @ Wed, 15 Apr 2020 22:57:33: end of X-cor INFO @ Wed, 15 Apr 2020 22:57:33: #2 finished! INFO @ Wed, 15 Apr 2020 22:57:33: #2 predicted fragment length is 168 bps INFO @ Wed, 15 Apr 2020 22:57:33: #2 alternative fragment length(s) may be 168 bps INFO @ Wed, 15 Apr 2020 22:57:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.10_model.r INFO @ Wed, 15 Apr 2020 22:57:33: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:57:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:57:34: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:57:36: 9000000 INFO @ Wed, 15 Apr 2020 22:57:43: 10000000 INFO @ Wed, 15 Apr 2020 22:57:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:57:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:57:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.05_summits.bed INFO @ Wed, 15 Apr 2020 22:57:48: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6404 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:57:49: 11000000 INFO @ Wed, 15 Apr 2020 22:57:56: 12000000 INFO @ Wed, 15 Apr 2020 22:58:01: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:58:01: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:58:01: #1 total tags in treatment: 12868098 INFO @ Wed, 15 Apr 2020 22:58:01: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:58:01: #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 22:58:02: #1 tags after filtering in treatment: 12868098 INFO @ Wed, 15 Apr 2020 22:58:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:58:02: #1 finished! INFO @ Wed, 15 Apr 2020 22:58:02: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:58:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:58:03: #2 number of paired peaks: 2487 INFO @ Wed, 15 Apr 2020 22:58:03: start model_add_line... INFO @ Wed, 15 Apr 2020 22:58:03: start X-correlation... INFO @ Wed, 15 Apr 2020 22:58:03: end of X-cor INFO @ Wed, 15 Apr 2020 22:58:03: #2 finished! INFO @ Wed, 15 Apr 2020 22:58:03: #2 predicted fragment length is 168 bps INFO @ Wed, 15 Apr 2020 22:58:03: #2 alternative fragment length(s) may be 168 bps INFO @ Wed, 15 Apr 2020 22:58:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.20_model.r INFO @ Wed, 15 Apr 2020 22:58:03: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:58:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:58:04: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:58:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:58:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:58:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.10_summits.bed INFO @ Wed, 15 Apr 2020 22:58:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4375 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:58:34: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 15 Apr 2020 22:58:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:58:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:58:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720171/SRX6720171.20_summits.bed INFO @ Wed, 15 Apr 2020 22:58:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2524 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。