Job ID = 6368692 SRX = SRX5402718 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:46 prefetch.2.10.7: 1) Downloading 'SRR8602952'... 2020-06-16T00:27:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:42 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:42 prefetch.2.10.7: 1) 'SRR8602952' was downloaded successfully Read 38462838 spots for SRR8602952/SRR8602952.sra Written 38462838 spots for SRR8602952/SRR8602952.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: 00:07:25 38462838 reads; of these: 38462838 (100.00%) were unpaired; of these: 7104151 (18.47%) aligned 0 times 27067189 (70.37%) aligned exactly 1 time 4291498 (11.16%) aligned >1 times 81.53% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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] 6999959 / 31358687 = 0.2232 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 09:49:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.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 09:49:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:41: 1000000 INFO @ Tue, 16 Jun 2020 09:49:46: 2000000 INFO @ Tue, 16 Jun 2020 09:49:52: 3000000 INFO @ Tue, 16 Jun 2020 09:49:57: 4000000 INFO @ Tue, 16 Jun 2020 09:50:03: 5000000 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 09:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.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 09:50:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:09: 6000000 INFO @ Tue, 16 Jun 2020 09:50:11: 1000000 INFO @ Tue, 16 Jun 2020 09:50:15: 7000000 INFO @ Tue, 16 Jun 2020 09:50:17: 2000000 INFO @ Tue, 16 Jun 2020 09:50:21: 8000000 INFO @ Tue, 16 Jun 2020 09:50:23: 3000000 INFO @ Tue, 16 Jun 2020 09:50:26: 9000000 INFO @ Tue, 16 Jun 2020 09:50:29: 4000000 INFO @ Tue, 16 Jun 2020 09:50:32: 10000000 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 09:50:35: 5000000 INFO @ Tue, 16 Jun 2020 09:50:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.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 09:50:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:38: 11000000 INFO @ Tue, 16 Jun 2020 09:50:41: 6000000 INFO @ Tue, 16 Jun 2020 09:50:42: 1000000 INFO @ Tue, 16 Jun 2020 09:50:45: 12000000 INFO @ Tue, 16 Jun 2020 09:50:47: 7000000 INFO @ Tue, 16 Jun 2020 09:50:48: 2000000 INFO @ Tue, 16 Jun 2020 09:50:51: 13000000 INFO @ Tue, 16 Jun 2020 09:50:54: 8000000 INFO @ Tue, 16 Jun 2020 09:50:54: 3000000 INFO @ Tue, 16 Jun 2020 09:50:57: 14000000 INFO @ Tue, 16 Jun 2020 09:51:00: 9000000 INFO @ Tue, 16 Jun 2020 09:51:01: 4000000 INFO @ Tue, 16 Jun 2020 09:51:03: 15000000 INFO @ Tue, 16 Jun 2020 09:51:06: 10000000 INFO @ Tue, 16 Jun 2020 09:51:07: 5000000 INFO @ Tue, 16 Jun 2020 09:51:10: 16000000 INFO @ Tue, 16 Jun 2020 09:51:12: 11000000 INFO @ Tue, 16 Jun 2020 09:51:13: 6000000 INFO @ Tue, 16 Jun 2020 09:51:16: 17000000 INFO @ Tue, 16 Jun 2020 09:51:18: 12000000 INFO @ Tue, 16 Jun 2020 09:51:19: 7000000 INFO @ Tue, 16 Jun 2020 09:51:22: 18000000 INFO @ Tue, 16 Jun 2020 09:51:25: 13000000 INFO @ Tue, 16 Jun 2020 09:51:25: 8000000 INFO @ Tue, 16 Jun 2020 09:51:28: 19000000 INFO @ Tue, 16 Jun 2020 09:51:31: 9000000 INFO @ Tue, 16 Jun 2020 09:51:31: 14000000 INFO @ Tue, 16 Jun 2020 09:51:34: 20000000 INFO @ Tue, 16 Jun 2020 09:51:37: 10000000 INFO @ Tue, 16 Jun 2020 09:51:38: 15000000 INFO @ Tue, 16 Jun 2020 09:51:40: 21000000 INFO @ Tue, 16 Jun 2020 09:51:43: 11000000 INFO @ Tue, 16 Jun 2020 09:51:44: 16000000 INFO @ Tue, 16 Jun 2020 09:51:46: 22000000 INFO @ Tue, 16 Jun 2020 09:51:49: 12000000 INFO @ Tue, 16 Jun 2020 09:51:51: 17000000 INFO @ Tue, 16 Jun 2020 09:51:52: 23000000 INFO @ Tue, 16 Jun 2020 09:51:56: 13000000 INFO @ Tue, 16 Jun 2020 09:51:58: 18000000 INFO @ Tue, 16 Jun 2020 09:51:58: 24000000 INFO @ Tue, 16 Jun 2020 09:52:01: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:01: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:01: #1 total tags in treatment: 24358728 INFO @ Tue, 16 Jun 2020 09:52:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:01: #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 09:52:01: #1 tags after filtering in treatment: 24358728 INFO @ Tue, 16 Jun 2020 09:52:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:02: 14000000 INFO @ Tue, 16 Jun 2020 09:52:03: #2 number of paired peaks: 132 WARNING @ Tue, 16 Jun 2020 09:52:03: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:03: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:52:03: #2 alternative fragment length(s) may be 1,12,44,480,585 bps INFO @ Tue, 16 Jun 2020 09:52:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.05_model.r WARNING @ Tue, 16 Jun 2020 09:52:03: #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 09:52:03: #2 You may need to consider one of the other alternative d(s): 1,12,44,480,585 WARNING @ Tue, 16 Jun 2020 09:52:03: #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 09:52:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:04: 19000000 INFO @ Tue, 16 Jun 2020 09:52:08: 15000000 INFO @ Tue, 16 Jun 2020 09:52:11: 20000000 INFO @ Tue, 16 Jun 2020 09:52:14: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:52:17: 21000000 INFO @ Tue, 16 Jun 2020 09:52:20: 17000000 INFO @ Tue, 16 Jun 2020 09:52:24: 22000000 INFO @ Tue, 16 Jun 2020 09:52:26: 18000000 INFO @ Tue, 16 Jun 2020 09:52:30: 23000000 INFO @ Tue, 16 Jun 2020 09:52:32: 19000000 INFO @ Tue, 16 Jun 2020 09:52:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:37: 24000000 INFO @ Tue, 16 Jun 2020 09:52:38: 20000000 INFO @ Tue, 16 Jun 2020 09:52:39: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:39: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:39: #1 total tags in treatment: 24358728 INFO @ Tue, 16 Jun 2020 09:52:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:39: #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 09:52:40: #1 tags after filtering in treatment: 24358728 INFO @ Tue, 16 Jun 2020 09:52:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:41: #2 number of paired peaks: 132 WARNING @ Tue, 16 Jun 2020 09:52:41: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:42: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:52:42: #2 alternative fragment length(s) may be 1,12,44,480,585 bps INFO @ Tue, 16 Jun 2020 09:52:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.10_model.r WARNING @ Tue, 16 Jun 2020 09:52:42: #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 09:52:42: #2 You may need to consider one of the other alternative d(s): 1,12,44,480,585 WARNING @ Tue, 16 Jun 2020 09:52:42: #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 09:52:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:44: 21000000 INFO @ Tue, 16 Jun 2020 09:52:50: 22000000 INFO @ Tue, 16 Jun 2020 09:52:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.05_summits.bed INFO @ Tue, 16 Jun 2020 09:52:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:56: 23000000 INFO @ Tue, 16 Jun 2020 09:53:02: 24000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:53:04: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:04: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:04: #1 total tags in treatment: 24358728 INFO @ Tue, 16 Jun 2020 09:53:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:04: #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 09:53:05: #1 tags after filtering in treatment: 24358728 INFO @ Tue, 16 Jun 2020 09:53:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:06: #2 number of paired peaks: 132 WARNING @ Tue, 16 Jun 2020 09:53:06: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:07: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:53:07: #2 alternative fragment length(s) may be 1,12,44,480,585 bps INFO @ Tue, 16 Jun 2020 09:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.20_model.r WARNING @ Tue, 16 Jun 2020 09:53:07: #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 09:53:07: #2 You may need to consider one of the other alternative d(s): 1,12,44,480,585 WARNING @ Tue, 16 Jun 2020 09:53:07: #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 09:53:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402718/SRX5402718.20_summits.bed INFO @ Tue, 16 Jun 2020 09:54:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling