Job ID = 6368978 SRX = SRX7971803 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:31 prefetch.2.10.7: 1) Downloading 'SRR11392689'... 2020-06-16T00:30:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:41 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:41 prefetch.2.10.7: 1) 'SRR11392689' was downloaded successfully Read 40364270 spots for SRR11392689/SRR11392689.sra Written 40364270 spots for SRR11392689/SRR11392689.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: 00:13:22 40364270 reads; of these: 40364270 (100.00%) were unpaired; of these: 1458572 (3.61%) aligned 0 times 29535973 (73.17%) aligned exactly 1 time 9369725 (23.21%) aligned >1 times 96.39% overall alignment rate Time searching: 00:13:22 Overall time: 00:13:22 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] 9486774 / 38905698 = 0.2438 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 10:01:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.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 10:01:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:01:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:01:49: 1000000 INFO @ Tue, 16 Jun 2020 10:01:55: 2000000 INFO @ Tue, 16 Jun 2020 10:02:02: 3000000 INFO @ Tue, 16 Jun 2020 10:02:07: 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 10:02:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.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 10:02:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:02:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:02:13: 5000000 INFO @ Tue, 16 Jun 2020 10:02:20: 1000000 INFO @ Tue, 16 Jun 2020 10:02:20: 6000000 INFO @ Tue, 16 Jun 2020 10:02:26: 7000000 INFO @ Tue, 16 Jun 2020 10:02:26: 2000000 INFO @ Tue, 16 Jun 2020 10:02:32: 8000000 INFO @ Tue, 16 Jun 2020 10:02:33: 3000000 INFO @ Tue, 16 Jun 2020 10:02:39: 9000000 INFO @ Tue, 16 Jun 2020 10:02:39: 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 @ Tue, 16 Jun 2020 10:02:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.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 10:02:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:02:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:02:45: 10000000 INFO @ Tue, 16 Jun 2020 10:02:46: 5000000 INFO @ Tue, 16 Jun 2020 10:02:51: 1000000 INFO @ Tue, 16 Jun 2020 10:02:52: 11000000 INFO @ Tue, 16 Jun 2020 10:02:53: 6000000 INFO @ Tue, 16 Jun 2020 10:02:58: 2000000 INFO @ Tue, 16 Jun 2020 10:02:59: 12000000 INFO @ Tue, 16 Jun 2020 10:02:59: 7000000 INFO @ Tue, 16 Jun 2020 10:03:05: 13000000 INFO @ Tue, 16 Jun 2020 10:03:06: 3000000 INFO @ Tue, 16 Jun 2020 10:03:06: 8000000 INFO @ Tue, 16 Jun 2020 10:03:12: 14000000 INFO @ Tue, 16 Jun 2020 10:03:13: 9000000 INFO @ Tue, 16 Jun 2020 10:03:13: 4000000 INFO @ Tue, 16 Jun 2020 10:03:19: 15000000 INFO @ Tue, 16 Jun 2020 10:03:20: 10000000 INFO @ Tue, 16 Jun 2020 10:03:21: 5000000 INFO @ Tue, 16 Jun 2020 10:03:26: 16000000 INFO @ Tue, 16 Jun 2020 10:03:27: 11000000 INFO @ Tue, 16 Jun 2020 10:03:28: 6000000 INFO @ Tue, 16 Jun 2020 10:03:33: 17000000 INFO @ Tue, 16 Jun 2020 10:03:34: 12000000 INFO @ Tue, 16 Jun 2020 10:03:36: 7000000 INFO @ Tue, 16 Jun 2020 10:03:40: 18000000 INFO @ Tue, 16 Jun 2020 10:03:41: 13000000 INFO @ Tue, 16 Jun 2020 10:03:43: 8000000 INFO @ Tue, 16 Jun 2020 10:03:47: 19000000 INFO @ Tue, 16 Jun 2020 10:03:48: 14000000 INFO @ Tue, 16 Jun 2020 10:03:51: 9000000 INFO @ Tue, 16 Jun 2020 10:03:53: 20000000 INFO @ Tue, 16 Jun 2020 10:03:55: 15000000 INFO @ Tue, 16 Jun 2020 10:03:58: 10000000 INFO @ Tue, 16 Jun 2020 10:04:00: 21000000 INFO @ Tue, 16 Jun 2020 10:04:02: 16000000 INFO @ Tue, 16 Jun 2020 10:04:06: 11000000 INFO @ Tue, 16 Jun 2020 10:04:07: 22000000 INFO @ Tue, 16 Jun 2020 10:04:09: 17000000 INFO @ Tue, 16 Jun 2020 10:04:14: 12000000 INFO @ Tue, 16 Jun 2020 10:04:14: 23000000 INFO @ Tue, 16 Jun 2020 10:04:16: 18000000 INFO @ Tue, 16 Jun 2020 10:04:21: 24000000 INFO @ Tue, 16 Jun 2020 10:04:21: 13000000 INFO @ Tue, 16 Jun 2020 10:04:22: 19000000 INFO @ Tue, 16 Jun 2020 10:04:28: 25000000 INFO @ Tue, 16 Jun 2020 10:04:29: 14000000 INFO @ Tue, 16 Jun 2020 10:04:29: 20000000 INFO @ Tue, 16 Jun 2020 10:04:35: 26000000 INFO @ Tue, 16 Jun 2020 10:04:36: 21000000 INFO @ Tue, 16 Jun 2020 10:04:37: 15000000 INFO @ Tue, 16 Jun 2020 10:04:42: 27000000 INFO @ Tue, 16 Jun 2020 10:04:43: 22000000 INFO @ Tue, 16 Jun 2020 10:04:44: 16000000 INFO @ Tue, 16 Jun 2020 10:04:48: 28000000 INFO @ Tue, 16 Jun 2020 10:04:50: 23000000 INFO @ Tue, 16 Jun 2020 10:04:52: 17000000 INFO @ Tue, 16 Jun 2020 10:04:55: 29000000 INFO @ Tue, 16 Jun 2020 10:04:57: 24000000 INFO @ Tue, 16 Jun 2020 10:04:58: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:04:58: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:04:58: #1 total tags in treatment: 29418924 INFO @ Tue, 16 Jun 2020 10:04:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:04:58: #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 10:04:59: #1 tags after filtering in treatment: 29418924 INFO @ Tue, 16 Jun 2020 10:04:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:04:59: #1 finished! INFO @ Tue, 16 Jun 2020 10:04:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:04:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:05:00: 18000000 INFO @ Tue, 16 Jun 2020 10:05:01: #2 number of paired peaks: 149 WARNING @ Tue, 16 Jun 2020 10:05:01: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 16 Jun 2020 10:05:01: start model_add_line... INFO @ Tue, 16 Jun 2020 10:05:01: start X-correlation... INFO @ Tue, 16 Jun 2020 10:05:01: end of X-cor INFO @ Tue, 16 Jun 2020 10:05:01: #2 finished! INFO @ Tue, 16 Jun 2020 10:05:01: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:05:01: #2 alternative fragment length(s) may be 1,23,38,66,591 bps INFO @ Tue, 16 Jun 2020 10:05:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.05_model.r WARNING @ Tue, 16 Jun 2020 10:05:01: #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 10:05:01: #2 You may need to consider one of the other alternative d(s): 1,23,38,66,591 WARNING @ Tue, 16 Jun 2020 10:05:01: #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 10:05:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:05:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:05:03: 25000000 INFO @ Tue, 16 Jun 2020 10:05:08: 19000000 INFO @ Tue, 16 Jun 2020 10:05:10: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:05:15: 20000000 INFO @ Tue, 16 Jun 2020 10:05:17: 27000000 INFO @ Tue, 16 Jun 2020 10:05:23: 21000000 INFO @ Tue, 16 Jun 2020 10:05:24: 28000000 INFO @ Tue, 16 Jun 2020 10:05:30: 29000000 INFO @ Tue, 16 Jun 2020 10:05:31: 22000000 INFO @ Tue, 16 Jun 2020 10:05:33: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:05:33: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:05:33: #1 total tags in treatment: 29418924 INFO @ Tue, 16 Jun 2020 10:05:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:05:33: #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 10:05:34: #1 tags after filtering in treatment: 29418924 INFO @ Tue, 16 Jun 2020 10:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:05:34: #1 finished! INFO @ Tue, 16 Jun 2020 10:05:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:05:36: #2 number of paired peaks: 149 WARNING @ Tue, 16 Jun 2020 10:05:36: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 16 Jun 2020 10:05:36: start model_add_line... INFO @ Tue, 16 Jun 2020 10:05:36: start X-correlation... INFO @ Tue, 16 Jun 2020 10:05:36: end of X-cor INFO @ Tue, 16 Jun 2020 10:05:36: #2 finished! INFO @ Tue, 16 Jun 2020 10:05:36: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:05:36: #2 alternative fragment length(s) may be 1,23,38,66,591 bps INFO @ Tue, 16 Jun 2020 10:05:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.10_model.r WARNING @ Tue, 16 Jun 2020 10:05:36: #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 10:05:36: #2 You may need to consider one of the other alternative d(s): 1,23,38,66,591 WARNING @ Tue, 16 Jun 2020 10:05:36: #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 10:05:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:05:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:05:38: 23000000 INFO @ Tue, 16 Jun 2020 10:05:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:05:46: 24000000 INFO @ Tue, 16 Jun 2020 10:05:53: 25000000 INFO @ Tue, 16 Jun 2020 10:05:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:05:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:05:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.05_summits.bed INFO @ Tue, 16 Jun 2020 10:05:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:06:00: 26000000 INFO @ Tue, 16 Jun 2020 10:06:08: 27000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:06:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:06:15: 28000000 INFO @ Tue, 16 Jun 2020 10:06:23: 29000000 INFO @ Tue, 16 Jun 2020 10:06:26: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:06:26: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:06:26: #1 total tags in treatment: 29418924 INFO @ Tue, 16 Jun 2020 10:06:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:06:26: #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 10:06:26: #1 tags after filtering in treatment: 29418924 INFO @ Tue, 16 Jun 2020 10:06:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:06:26: #1 finished! INFO @ Tue, 16 Jun 2020 10:06:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:06:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:06:28: #2 number of paired peaks: 149 WARNING @ Tue, 16 Jun 2020 10:06:28: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 16 Jun 2020 10:06:28: start model_add_line... INFO @ Tue, 16 Jun 2020 10:06:29: start X-correlation... INFO @ Tue, 16 Jun 2020 10:06:29: end of X-cor INFO @ Tue, 16 Jun 2020 10:06:29: #2 finished! INFO @ Tue, 16 Jun 2020 10:06:29: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:06:29: #2 alternative fragment length(s) may be 1,23,38,66,591 bps INFO @ Tue, 16 Jun 2020 10:06:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.20_model.r WARNING @ Tue, 16 Jun 2020 10:06:29: #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 10:06:29: #2 You may need to consider one of the other alternative d(s): 1,23,38,66,591 WARNING @ Tue, 16 Jun 2020 10:06:29: #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 10:06:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:06:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:06:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:06:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:06:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.10_summits.bed INFO @ Tue, 16 Jun 2020 10:06:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:07:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:07:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:07:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:07:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971803/SRX7971803.20_summits.bed INFO @ Tue, 16 Jun 2020 10:07:27: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling