Job ID = 6367634 SRX = SRX3583346 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:28:21 prefetch.2.10.7: 1) Downloading 'SRR6494002'... 2020-06-15T23:28:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:23 prefetch.2.10.7: 1) 'SRR6494002' was downloaded successfully 2020-06-15T23:36:23 prefetch.2.10.7: 'SRR6494002' has 0 unresolved dependencies Read 37460851 spots for SRR6494002/SRR6494002.sra Written 37460851 spots for SRR6494002/SRR6494002.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: 00:11:53 37460851 reads; of these: 37460851 (100.00%) were unpaired; of these: 3719075 (9.93%) aligned 0 times 28246988 (75.40%) aligned exactly 1 time 5494788 (14.67%) aligned >1 times 90.07% overall alignment rate Time searching: 00:11:53 Overall time: 00:11:53 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] 8520730 / 33741776 = 0.2525 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 08:58:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.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 08:58:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:07: 1000000 INFO @ Tue, 16 Jun 2020 08:58:13: 2000000 INFO @ Tue, 16 Jun 2020 08:58:19: 3000000 INFO @ Tue, 16 Jun 2020 08:58:26: 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 08:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.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 08:58:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:32: 5000000 INFO @ Tue, 16 Jun 2020 08:58:39: 1000000 INFO @ Tue, 16 Jun 2020 08:58:40: 6000000 INFO @ Tue, 16 Jun 2020 08:58:47: 2000000 INFO @ Tue, 16 Jun 2020 08:58:47: 7000000 INFO @ Tue, 16 Jun 2020 08:58:55: 3000000 INFO @ Tue, 16 Jun 2020 08:58:55: 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 08:59:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.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 08:59:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:02: 9000000 INFO @ Tue, 16 Jun 2020 08:59:02: 4000000 INFO @ Tue, 16 Jun 2020 08:59:09: 1000000 INFO @ Tue, 16 Jun 2020 08:59:09: 10000000 INFO @ Tue, 16 Jun 2020 08:59:09: 5000000 INFO @ Tue, 16 Jun 2020 08:59:16: 2000000 INFO @ Tue, 16 Jun 2020 08:59:17: 11000000 INFO @ Tue, 16 Jun 2020 08:59:17: 6000000 INFO @ Tue, 16 Jun 2020 08:59:24: 3000000 INFO @ Tue, 16 Jun 2020 08:59:24: 7000000 INFO @ Tue, 16 Jun 2020 08:59:24: 12000000 INFO @ Tue, 16 Jun 2020 08:59:31: 8000000 INFO @ Tue, 16 Jun 2020 08:59:31: 13000000 INFO @ Tue, 16 Jun 2020 08:59:31: 4000000 INFO @ Tue, 16 Jun 2020 08:59:39: 9000000 INFO @ Tue, 16 Jun 2020 08:59:39: 14000000 INFO @ Tue, 16 Jun 2020 08:59:39: 5000000 INFO @ Tue, 16 Jun 2020 08:59:46: 10000000 INFO @ Tue, 16 Jun 2020 08:59:46: 15000000 INFO @ Tue, 16 Jun 2020 08:59:46: 6000000 INFO @ Tue, 16 Jun 2020 08:59:53: 11000000 INFO @ Tue, 16 Jun 2020 08:59:53: 16000000 INFO @ Tue, 16 Jun 2020 08:59:54: 7000000 INFO @ Tue, 16 Jun 2020 09:00:01: 12000000 INFO @ Tue, 16 Jun 2020 09:00:01: 17000000 INFO @ Tue, 16 Jun 2020 09:00:01: 8000000 INFO @ Tue, 16 Jun 2020 09:00:08: 13000000 INFO @ Tue, 16 Jun 2020 09:00:08: 18000000 INFO @ Tue, 16 Jun 2020 09:00:09: 9000000 INFO @ Tue, 16 Jun 2020 09:00:15: 14000000 INFO @ Tue, 16 Jun 2020 09:00:15: 19000000 INFO @ Tue, 16 Jun 2020 09:00:16: 10000000 INFO @ Tue, 16 Jun 2020 09:00:22: 15000000 INFO @ Tue, 16 Jun 2020 09:00:22: 20000000 INFO @ Tue, 16 Jun 2020 09:00:23: 11000000 INFO @ Tue, 16 Jun 2020 09:00:29: 16000000 INFO @ Tue, 16 Jun 2020 09:00:29: 21000000 INFO @ Tue, 16 Jun 2020 09:00:30: 12000000 INFO @ Tue, 16 Jun 2020 09:00:36: 17000000 INFO @ Tue, 16 Jun 2020 09:00:37: 22000000 INFO @ Tue, 16 Jun 2020 09:00:37: 13000000 INFO @ Tue, 16 Jun 2020 09:00:44: 18000000 INFO @ Tue, 16 Jun 2020 09:00:44: 23000000 INFO @ Tue, 16 Jun 2020 09:00:45: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:00:51: 19000000 INFO @ Tue, 16 Jun 2020 09:00:51: 24000000 INFO @ Tue, 16 Jun 2020 09:00:52: 15000000 INFO @ Tue, 16 Jun 2020 09:00:58: 20000000 INFO @ Tue, 16 Jun 2020 09:00:58: 25000000 INFO @ Tue, 16 Jun 2020 09:00:59: 16000000 INFO @ Tue, 16 Jun 2020 09:01:00: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:01:00: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:01:00: #1 total tags in treatment: 25221046 INFO @ Tue, 16 Jun 2020 09:01:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:00: #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 09:01:00: #1 tags after filtering in treatment: 25221046 INFO @ Tue, 16 Jun 2020 09:01:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:01:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:02: #2 number of paired peaks: 132 WARNING @ Tue, 16 Jun 2020 09:01:02: 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 09:01:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:02: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:01:02: #2 alternative fragment length(s) may be 1,39 bps INFO @ Tue, 16 Jun 2020 09:01:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.05_model.r WARNING @ Tue, 16 Jun 2020 09:01:02: #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 09:01:02: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Tue, 16 Jun 2020 09:01:02: #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 09:01:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:05: 21000000 INFO @ Tue, 16 Jun 2020 09:01:06: 17000000 INFO @ Tue, 16 Jun 2020 09:01:12: 22000000 INFO @ Tue, 16 Jun 2020 09:01:13: 18000000 INFO @ Tue, 16 Jun 2020 09:01:19: 23000000 INFO @ Tue, 16 Jun 2020 09:01:21: 19000000 INFO @ Tue, 16 Jun 2020 09:01:26: 24000000 INFO @ Tue, 16 Jun 2020 09:01:28: 20000000 INFO @ Tue, 16 Jun 2020 09:01:33: 25000000 INFO @ Tue, 16 Jun 2020 09:01:35: 21000000 INFO @ Tue, 16 Jun 2020 09:01:35: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:01:35: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:01:35: #1 total tags in treatment: 25221046 INFO @ Tue, 16 Jun 2020 09:01:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:35: #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 09:01:35: #1 tags after filtering in treatment: 25221046 INFO @ Tue, 16 Jun 2020 09:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:01:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:37: #2 number of paired peaks: 132 WARNING @ Tue, 16 Jun 2020 09:01:37: 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 09:01:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:37: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:01:37: #2 alternative fragment length(s) may be 1,39 bps INFO @ Tue, 16 Jun 2020 09:01:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.10_model.r WARNING @ Tue, 16 Jun 2020 09:01:37: #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 09:01:37: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Tue, 16 Jun 2020 09:01:37: #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 09:01:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:42: 22000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:01:48: 23000000 INFO @ Tue, 16 Jun 2020 09:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.05_summits.bed INFO @ Tue, 16 Jun 2020 09:01:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:01:55: 24000000 INFO @ Tue, 16 Jun 2020 09:02:02: 25000000 INFO @ Tue, 16 Jun 2020 09:02:03: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:02:03: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:02:03: #1 total tags in treatment: 25221046 INFO @ Tue, 16 Jun 2020 09:02:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:03: #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 09:02:04: #1 tags after filtering in treatment: 25221046 INFO @ Tue, 16 Jun 2020 09:02:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:05: #2 number of paired peaks: 132 WARNING @ Tue, 16 Jun 2020 09:02:05: 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 09:02:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:05: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:02:05: #2 alternative fragment length(s) may be 1,39 bps INFO @ Tue, 16 Jun 2020 09:02:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.20_model.r WARNING @ Tue, 16 Jun 2020 09:02:05: #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 09:02:05: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Tue, 16 Jun 2020 09:02:05: #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 09:02:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.10_summits.bed INFO @ Tue, 16 Jun 2020 09:02:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:02:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583346/SRX3583346.20_summits.bed INFO @ Tue, 16 Jun 2020 09:02:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling