Job ID = 6368977 SRX = SRX7971802 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:48:28 prefetch.2.10.7: 1) Downloading 'SRR11392688'... 2020-06-16T00:48:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:53:00 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:53:00 prefetch.2.10.7: 1) 'SRR11392688' was downloaded successfully Read 32221758 spots for SRR11392688/SRR11392688.sra Written 32221758 spots for SRR11392688/SRR11392688.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: 00:11:17 32221758 reads; of these: 32221758 (100.00%) were unpaired; of these: 1325539 (4.11%) aligned 0 times 23555201 (73.10%) aligned exactly 1 time 7341018 (22.78%) aligned >1 times 95.89% overall alignment rate Time searching: 00:11:17 Overall time: 00:11:17 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] 6948129 / 30896219 = 0.2249 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 @ Tue, 16 Jun 2020 10:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.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 @ Tue, 16 Jun 2020 10:15:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:15:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:15:22: 1000000 INFO @ Tue, 16 Jun 2020 10:15:28: 2000000 INFO @ Tue, 16 Jun 2020 10:15:34: 3000000 INFO @ Tue, 16 Jun 2020 10:15:41: 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 @ Tue, 16 Jun 2020 10:15:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.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 @ Tue, 16 Jun 2020 10:15:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:15:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:15:48: 5000000 INFO @ Tue, 16 Jun 2020 10:15:53: 1000000 INFO @ Tue, 16 Jun 2020 10:15:55: 6000000 INFO @ Tue, 16 Jun 2020 10:16:01: 2000000 INFO @ Tue, 16 Jun 2020 10:16:02: 7000000 INFO @ Tue, 16 Jun 2020 10:16:09: 3000000 INFO @ Tue, 16 Jun 2020 10:16:10: 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 @ Tue, 16 Jun 2020 10:16:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.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 @ Tue, 16 Jun 2020 10:16:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:16:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:16:17: 4000000 INFO @ Tue, 16 Jun 2020 10:16:17: 9000000 INFO @ Tue, 16 Jun 2020 10:16:24: 1000000 INFO @ Tue, 16 Jun 2020 10:16:25: 10000000 INFO @ Tue, 16 Jun 2020 10:16:25: 5000000 INFO @ Tue, 16 Jun 2020 10:16:32: 2000000 INFO @ Tue, 16 Jun 2020 10:16:32: 11000000 INFO @ Tue, 16 Jun 2020 10:16:33: 6000000 INFO @ Tue, 16 Jun 2020 10:16:40: 3000000 INFO @ Tue, 16 Jun 2020 10:16:40: 12000000 INFO @ Tue, 16 Jun 2020 10:16:41: 7000000 INFO @ Tue, 16 Jun 2020 10:16:47: 13000000 INFO @ Tue, 16 Jun 2020 10:16:48: 4000000 INFO @ Tue, 16 Jun 2020 10:16:49: 8000000 INFO @ Tue, 16 Jun 2020 10:16:55: 14000000 INFO @ Tue, 16 Jun 2020 10:16:56: 5000000 INFO @ Tue, 16 Jun 2020 10:16:58: 9000000 INFO @ Tue, 16 Jun 2020 10:17:03: 15000000 INFO @ Tue, 16 Jun 2020 10:17:04: 6000000 INFO @ Tue, 16 Jun 2020 10:17:06: 10000000 INFO @ Tue, 16 Jun 2020 10:17:10: 16000000 INFO @ Tue, 16 Jun 2020 10:17:12: 7000000 INFO @ Tue, 16 Jun 2020 10:17:14: 11000000 INFO @ Tue, 16 Jun 2020 10:17:18: 17000000 INFO @ Tue, 16 Jun 2020 10:17:20: 8000000 INFO @ Tue, 16 Jun 2020 10:17:23: 12000000 INFO @ Tue, 16 Jun 2020 10:17:26: 18000000 INFO @ Tue, 16 Jun 2020 10:17:28: 9000000 INFO @ Tue, 16 Jun 2020 10:17:31: 13000000 INFO @ Tue, 16 Jun 2020 10:17:33: 19000000 INFO @ Tue, 16 Jun 2020 10:17:36: 10000000 INFO @ Tue, 16 Jun 2020 10:17:39: 14000000 INFO @ Tue, 16 Jun 2020 10:17:41: 20000000 INFO @ Tue, 16 Jun 2020 10:17:44: 11000000 INFO @ Tue, 16 Jun 2020 10:17:47: 15000000 INFO @ Tue, 16 Jun 2020 10:17:48: 21000000 INFO @ Tue, 16 Jun 2020 10:17:52: 12000000 INFO @ Tue, 16 Jun 2020 10:17:56: 16000000 INFO @ Tue, 16 Jun 2020 10:17:56: 22000000 INFO @ Tue, 16 Jun 2020 10:18:01: 13000000 INFO @ Tue, 16 Jun 2020 10:18:04: 23000000 INFO @ Tue, 16 Jun 2020 10:18:04: 17000000 INFO @ Tue, 16 Jun 2020 10:18:09: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:18:11: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:18:11: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:18:11: #1 total tags in treatment: 23948090 INFO @ Tue, 16 Jun 2020 10:18:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:18:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:18:12: #1 tags after filtering in treatment: 23948090 INFO @ Tue, 16 Jun 2020 10:18:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:18:12: #1 finished! INFO @ Tue, 16 Jun 2020 10:18:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:18:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:18:12: 18000000 INFO @ Tue, 16 Jun 2020 10:18:13: #2 number of paired peaks: 239 WARNING @ Tue, 16 Jun 2020 10:18:13: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Tue, 16 Jun 2020 10:18:13: start model_add_line... INFO @ Tue, 16 Jun 2020 10:18:13: start X-correlation... INFO @ Tue, 16 Jun 2020 10:18:13: end of X-cor INFO @ Tue, 16 Jun 2020 10:18:13: #2 finished! INFO @ Tue, 16 Jun 2020 10:18:13: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:18:13: #2 alternative fragment length(s) may be 1,23,67,588 bps INFO @ Tue, 16 Jun 2020 10:18:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.05_model.r WARNING @ Tue, 16 Jun 2020 10:18:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:18:13: #2 You may need to consider one of the other alternative d(s): 1,23,67,588 WARNING @ Tue, 16 Jun 2020 10:18:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:18:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:18:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:18:17: 15000000 INFO @ Tue, 16 Jun 2020 10:18:21: 19000000 INFO @ Tue, 16 Jun 2020 10:18:26: 16000000 INFO @ Tue, 16 Jun 2020 10:18:29: 20000000 INFO @ Tue, 16 Jun 2020 10:18:34: 17000000 INFO @ Tue, 16 Jun 2020 10:18:38: 21000000 INFO @ Tue, 16 Jun 2020 10:18:43: 18000000 INFO @ Tue, 16 Jun 2020 10:18:46: 22000000 INFO @ Tue, 16 Jun 2020 10:18:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:18:51: 19000000 INFO @ Tue, 16 Jun 2020 10:18:55: 23000000 INFO @ Tue, 16 Jun 2020 10:19:00: 20000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:19:03: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:19:03: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:19:03: #1 total tags in treatment: 23948090 INFO @ Tue, 16 Jun 2020 10:19:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:19:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:19:04: #1 tags after filtering in treatment: 23948090 INFO @ Tue, 16 Jun 2020 10:19:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:19:04: #1 finished! INFO @ Tue, 16 Jun 2020 10:19:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:19:05: #2 number of paired peaks: 239 WARNING @ Tue, 16 Jun 2020 10:19:05: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Tue, 16 Jun 2020 10:19:05: start model_add_line... INFO @ Tue, 16 Jun 2020 10:19:06: start X-correlation... INFO @ Tue, 16 Jun 2020 10:19:06: end of X-cor INFO @ Tue, 16 Jun 2020 10:19:06: #2 finished! INFO @ Tue, 16 Jun 2020 10:19:06: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:19:06: #2 alternative fragment length(s) may be 1,23,67,588 bps INFO @ Tue, 16 Jun 2020 10:19:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.10_model.r WARNING @ Tue, 16 Jun 2020 10:19:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:19:06: #2 You may need to consider one of the other alternative d(s): 1,23,67,588 WARNING @ Tue, 16 Jun 2020 10:19:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:19:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:19:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:19:08: 21000000 INFO @ Tue, 16 Jun 2020 10:19:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.05_summits.bed INFO @ Tue, 16 Jun 2020 10:19:09: Done! pass1 - making usageList (0 chroms): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:19:15: 22000000 INFO @ Tue, 16 Jun 2020 10:19:23: 23000000 INFO @ Tue, 16 Jun 2020 10:19:31: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:19:31: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:19:31: #1 total tags in treatment: 23948090 INFO @ Tue, 16 Jun 2020 10:19:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:19:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:19:31: #1 tags after filtering in treatment: 23948090 INFO @ Tue, 16 Jun 2020 10:19:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:19:31: #1 finished! INFO @ Tue, 16 Jun 2020 10:19:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:19:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:19:33: #2 number of paired peaks: 239 WARNING @ Tue, 16 Jun 2020 10:19:33: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Tue, 16 Jun 2020 10:19:33: start model_add_line... INFO @ Tue, 16 Jun 2020 10:19:33: start X-correlation... INFO @ Tue, 16 Jun 2020 10:19:33: end of X-cor INFO @ Tue, 16 Jun 2020 10:19:33: #2 finished! INFO @ Tue, 16 Jun 2020 10:19:33: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:19:33: #2 alternative fragment length(s) may be 1,23,67,588 bps INFO @ Tue, 16 Jun 2020 10:19:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.20_model.r WARNING @ Tue, 16 Jun 2020 10:19:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:19:33: #2 You may need to consider one of the other alternative d(s): 1,23,67,588 WARNING @ Tue, 16 Jun 2020 10:19:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:19:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:19:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:19:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.10_summits.bed INFO @ Tue, 16 Jun 2020 10:20:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:20:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:20:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:20:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:20:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971802/SRX7971802.20_summits.bed INFO @ Tue, 16 Jun 2020 10:20:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling