Job ID = 6507839 SRX = SRX494838 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:28:48 prefetch.2.10.7: 1) Downloading 'SRR1198370'... 2020-06-26T13:28:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:31:36 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:31:36 prefetch.2.10.7: 1) 'SRR1198370' was downloaded successfully Read 33596184 spots for SRR1198370/SRR1198370.sra Written 33596184 spots for SRR1198370/SRR1198370.sra 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: 00:08:28 33596184 reads; of these: 33596184 (100.00%) were unpaired; of these: 1331013 (3.96%) aligned 0 times 26715478 (79.52%) aligned exactly 1 time 5549693 (16.52%) aligned >1 times 96.04% overall alignment rate Time searching: 00:08:28 Overall time: 00:08:28 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 16 files... [bam_rmdupse_core] 8276409 / 32265171 = 0.2565 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 @ Fri, 26 Jun 2020 22:50:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.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 @ Fri, 26 Jun 2020 22:50:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:50:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:50:13: 1000000 INFO @ Fri, 26 Jun 2020 22:50:20: 2000000 INFO @ Fri, 26 Jun 2020 22:50:26: 3000000 INFO @ Fri, 26 Jun 2020 22:50:33: 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 @ Fri, 26 Jun 2020 22:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.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 @ Fri, 26 Jun 2020 22:50:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:50:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:50:39: 5000000 INFO @ Fri, 26 Jun 2020 22:50:44: 1000000 INFO @ Fri, 26 Jun 2020 22:50:47: 6000000 INFO @ Fri, 26 Jun 2020 22:50:51: 2000000 INFO @ Fri, 26 Jun 2020 22:50:54: 7000000 INFO @ Fri, 26 Jun 2020 22:50:59: 3000000 INFO @ Fri, 26 Jun 2020 22:51:01: 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 @ Fri, 26 Jun 2020 22:51:06: 4000000 INFO @ Fri, 26 Jun 2020 22:51:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.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 @ Fri, 26 Jun 2020 22:51:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:51:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:51:08: 9000000 INFO @ Fri, 26 Jun 2020 22:51:13: 5000000 INFO @ Fri, 26 Jun 2020 22:51:14: 1000000 INFO @ Fri, 26 Jun 2020 22:51:16: 10000000 INFO @ Fri, 26 Jun 2020 22:51:21: 6000000 INFO @ Fri, 26 Jun 2020 22:51:21: 2000000 INFO @ Fri, 26 Jun 2020 22:51:23: 11000000 INFO @ Fri, 26 Jun 2020 22:51:28: 7000000 INFO @ Fri, 26 Jun 2020 22:51:29: 3000000 INFO @ Fri, 26 Jun 2020 22:51:30: 12000000 INFO @ Fri, 26 Jun 2020 22:51:35: 8000000 INFO @ Fri, 26 Jun 2020 22:51:36: 4000000 INFO @ Fri, 26 Jun 2020 22:51:38: 13000000 INFO @ Fri, 26 Jun 2020 22:51:43: 9000000 INFO @ Fri, 26 Jun 2020 22:51:44: 5000000 INFO @ Fri, 26 Jun 2020 22:51:46: 14000000 INFO @ Fri, 26 Jun 2020 22:51:50: 10000000 INFO @ Fri, 26 Jun 2020 22:51:51: 6000000 INFO @ Fri, 26 Jun 2020 22:51:54: 15000000 INFO @ Fri, 26 Jun 2020 22:51:58: 11000000 INFO @ Fri, 26 Jun 2020 22:51:59: 7000000 INFO @ Fri, 26 Jun 2020 22:52:02: 16000000 INFO @ Fri, 26 Jun 2020 22:52:05: 12000000 INFO @ Fri, 26 Jun 2020 22:52:06: 8000000 INFO @ Fri, 26 Jun 2020 22:52:10: 17000000 INFO @ Fri, 26 Jun 2020 22:52:12: 13000000 INFO @ Fri, 26 Jun 2020 22:52:14: 9000000 INFO @ Fri, 26 Jun 2020 22:52:18: 18000000 INFO @ Fri, 26 Jun 2020 22:52:20: 14000000 INFO @ Fri, 26 Jun 2020 22:52:21: 10000000 INFO @ Fri, 26 Jun 2020 22:52:25: 19000000 INFO @ Fri, 26 Jun 2020 22:52:27: 15000000 INFO @ Fri, 26 Jun 2020 22:52:28: 11000000 INFO @ Fri, 26 Jun 2020 22:52:33: 20000000 INFO @ Fri, 26 Jun 2020 22:52:34: 16000000 INFO @ Fri, 26 Jun 2020 22:52:36: 12000000 INFO @ Fri, 26 Jun 2020 22:52:41: 21000000 INFO @ Fri, 26 Jun 2020 22:52:41: 17000000 INFO @ Fri, 26 Jun 2020 22:52:43: 13000000 INFO @ Fri, 26 Jun 2020 22:52:48: 22000000 INFO @ Fri, 26 Jun 2020 22:52:49: 18000000 INFO @ Fri, 26 Jun 2020 22:52:51: 14000000 INFO @ Fri, 26 Jun 2020 22:52:56: 19000000 INFO @ Fri, 26 Jun 2020 22:52:56: 23000000 INFO @ Fri, 26 Jun 2020 22:52:58: 15000000 INFO @ Fri, 26 Jun 2020 22:53:03: 20000000 INFO @ Fri, 26 Jun 2020 22:53:04: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:53:04: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:53:04: #1 total tags in treatment: 23988762 INFO @ Fri, 26 Jun 2020 22:53:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:53:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:53:04: #1 tags after filtering in treatment: 23988762 INFO @ Fri, 26 Jun 2020 22:53:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:53:04: #1 finished! INFO @ Fri, 26 Jun 2020 22:53:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:53:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:53:06: 16000000 INFO @ Fri, 26 Jun 2020 22:53:06: #2 number of paired peaks: 183 WARNING @ Fri, 26 Jun 2020 22:53:06: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 26 Jun 2020 22:53:06: start model_add_line... INFO @ Fri, 26 Jun 2020 22:53:06: start X-correlation... INFO @ Fri, 26 Jun 2020 22:53:06: end of X-cor INFO @ Fri, 26 Jun 2020 22:53:06: #2 finished! INFO @ Fri, 26 Jun 2020 22:53:06: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:53:06: #2 alternative fragment length(s) may be 1,14,555,570,573,587 bps INFO @ Fri, 26 Jun 2020 22:53:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.05_model.r WARNING @ Fri, 26 Jun 2020 22:53:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:53:06: #2 You may need to consider one of the other alternative d(s): 1,14,555,570,573,587 WARNING @ Fri, 26 Jun 2020 22:53:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:53:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:53:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:53:10: 21000000 INFO @ Fri, 26 Jun 2020 22:53:13: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:53:18: 22000000 INFO @ Fri, 26 Jun 2020 22:53:20: 18000000 INFO @ Fri, 26 Jun 2020 22:53:25: 23000000 INFO @ Fri, 26 Jun 2020 22:53:28: 19000000 INFO @ Fri, 26 Jun 2020 22:53:32: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:53:32: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:53:32: #1 total tags in treatment: 23988762 INFO @ Fri, 26 Jun 2020 22:53:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:53:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:53:32: #1 tags after filtering in treatment: 23988762 INFO @ Fri, 26 Jun 2020 22:53:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:53:32: #1 finished! INFO @ Fri, 26 Jun 2020 22:53:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:53:34: #2 number of paired peaks: 183 WARNING @ Fri, 26 Jun 2020 22:53:34: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 26 Jun 2020 22:53:34: start model_add_line... INFO @ Fri, 26 Jun 2020 22:53:34: start X-correlation... INFO @ Fri, 26 Jun 2020 22:53:34: end of X-cor INFO @ Fri, 26 Jun 2020 22:53:34: #2 finished! INFO @ Fri, 26 Jun 2020 22:53:34: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:53:34: #2 alternative fragment length(s) may be 1,14,555,570,573,587 bps INFO @ Fri, 26 Jun 2020 22:53:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.10_model.r WARNING @ Fri, 26 Jun 2020 22:53:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:53:34: #2 You may need to consider one of the other alternative d(s): 1,14,555,570,573,587 WARNING @ Fri, 26 Jun 2020 22:53:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:53:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:53:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:53:35: 20000000 INFO @ Fri, 26 Jun 2020 22:53:42: 21000000 INFO @ Fri, 26 Jun 2020 22:53:48: 22000000 INFO @ Fri, 26 Jun 2020 22:53:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:53:55: 23000000 INFO @ Fri, 26 Jun 2020 22:54:02: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:54:02: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:54:02: #1 total tags in treatment: 23988762 INFO @ Fri, 26 Jun 2020 22:54:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:54:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:54:02: #1 tags after filtering in treatment: 23988762 INFO @ Fri, 26 Jun 2020 22:54:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:54:02: #1 finished! INFO @ Fri, 26 Jun 2020 22:54:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:54:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:54:04: #2 number of paired peaks: 183 WARNING @ Fri, 26 Jun 2020 22:54:04: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 26 Jun 2020 22:54:04: start model_add_line... INFO @ Fri, 26 Jun 2020 22:54:04: start X-correlation... INFO @ Fri, 26 Jun 2020 22:54:04: end of X-cor INFO @ Fri, 26 Jun 2020 22:54:04: #2 finished! INFO @ Fri, 26 Jun 2020 22:54:04: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:54:04: #2 alternative fragment length(s) may be 1,14,555,570,573,587 bps INFO @ Fri, 26 Jun 2020 22:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.20_model.r WARNING @ Fri, 26 Jun 2020 22:54:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:54:04: #2 You may need to consider one of the other alternative d(s): 1,14,555,570,573,587 WARNING @ Fri, 26 Jun 2020 22:54:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:54:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:54:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:54:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:54:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:54:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.05_summits.bed INFO @ Fri, 26 Jun 2020 22:54:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:54:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:54:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:54:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:54:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.10_summits.bed INFO @ Fri, 26 Jun 2020 22:54:37: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:54:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:55:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:55:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:55:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494838/SRX494838.20_summits.bed INFO @ Fri, 26 Jun 2020 22:55:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling