Job ID = 6367161 SRX = SRX2965735 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:49:03 prefetch.2.10.7: 1) Downloading 'SRR5766320'... 2020-06-15T23:49:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:55:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:55:11 prefetch.2.10.7: 1) 'SRR5766320' was downloaded successfully 2020-06-15T23:55:11 prefetch.2.10.7: 'SRR5766320' has 0 unresolved dependencies Read 45844906 spots for SRR5766320/SRR5766320.sra Written 45844906 spots for SRR5766320/SRR5766320.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: 00:16:09 45844906 reads; of these: 45844906 (100.00%) were unpaired; of these: 5562532 (12.13%) aligned 0 times 33530558 (73.14%) aligned exactly 1 time 6751816 (14.73%) aligned >1 times 87.87% overall alignment rate Time searching: 00:16:09 Overall time: 00:16:09 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 20 files... [bam_rmdupse_core] 10512986 / 40282374 = 0.2610 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 09:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.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 09:26:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:02: 1000000 INFO @ Tue, 16 Jun 2020 09:27:10: 2000000 INFO @ Tue, 16 Jun 2020 09:27:18: 3000000 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 09:27:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.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 09:27:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:27: 4000000 INFO @ Tue, 16 Jun 2020 09:27:34: 1000000 INFO @ Tue, 16 Jun 2020 09:27:36: 5000000 INFO @ Tue, 16 Jun 2020 09:27:44: 2000000 INFO @ Tue, 16 Jun 2020 09:27:45: 6000000 INFO @ Tue, 16 Jun 2020 09:27:52: 3000000 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 09:27:54: 7000000 INFO @ Tue, 16 Jun 2020 09:27:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.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 09:27:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:01: 4000000 INFO @ Tue, 16 Jun 2020 09:28:04: 1000000 INFO @ Tue, 16 Jun 2020 09:28:04: 8000000 INFO @ Tue, 16 Jun 2020 09:28:10: 5000000 INFO @ Tue, 16 Jun 2020 09:28:13: 2000000 INFO @ Tue, 16 Jun 2020 09:28:14: 9000000 INFO @ Tue, 16 Jun 2020 09:28:20: 6000000 INFO @ Tue, 16 Jun 2020 09:28:23: 3000000 INFO @ Tue, 16 Jun 2020 09:28:24: 10000000 INFO @ Tue, 16 Jun 2020 09:28:29: 7000000 INFO @ Tue, 16 Jun 2020 09:28:32: 4000000 INFO @ Tue, 16 Jun 2020 09:28:34: 11000000 INFO @ Tue, 16 Jun 2020 09:28:39: 8000000 INFO @ Tue, 16 Jun 2020 09:28:42: 5000000 INFO @ Tue, 16 Jun 2020 09:28:44: 12000000 INFO @ Tue, 16 Jun 2020 09:28:48: 9000000 INFO @ Tue, 16 Jun 2020 09:28:51: 6000000 INFO @ Tue, 16 Jun 2020 09:28:54: 13000000 INFO @ Tue, 16 Jun 2020 09:28:58: 10000000 INFO @ Tue, 16 Jun 2020 09:29:01: 7000000 INFO @ Tue, 16 Jun 2020 09:29:04: 14000000 INFO @ Tue, 16 Jun 2020 09:29:07: 11000000 INFO @ Tue, 16 Jun 2020 09:29:10: 8000000 INFO @ Tue, 16 Jun 2020 09:29:14: 15000000 INFO @ Tue, 16 Jun 2020 09:29:16: 12000000 INFO @ Tue, 16 Jun 2020 09:29:19: 9000000 INFO @ Tue, 16 Jun 2020 09:29:24: 16000000 INFO @ Tue, 16 Jun 2020 09:29:25: 13000000 INFO @ Tue, 16 Jun 2020 09:29:28: 10000000 INFO @ Tue, 16 Jun 2020 09:29:34: 17000000 INFO @ Tue, 16 Jun 2020 09:29:34: 14000000 INFO @ Tue, 16 Jun 2020 09:29:37: 11000000 INFO @ Tue, 16 Jun 2020 09:29:43: 18000000 INFO @ Tue, 16 Jun 2020 09:29:44: 15000000 INFO @ Tue, 16 Jun 2020 09:29:47: 12000000 INFO @ Tue, 16 Jun 2020 09:29:52: 19000000 INFO @ Tue, 16 Jun 2020 09:29:53: 16000000 INFO @ Tue, 16 Jun 2020 09:29:57: 13000000 INFO @ Tue, 16 Jun 2020 09:30:02: 20000000 INFO @ Tue, 16 Jun 2020 09:30:02: 17000000 INFO @ Tue, 16 Jun 2020 09:30:07: 14000000 INFO @ Tue, 16 Jun 2020 09:30:11: 21000000 INFO @ Tue, 16 Jun 2020 09:30:11: 18000000 INFO @ Tue, 16 Jun 2020 09:30:16: 15000000 INFO @ Tue, 16 Jun 2020 09:30:20: 22000000 INFO @ Tue, 16 Jun 2020 09:30:21: 19000000 INFO @ Tue, 16 Jun 2020 09:30:25: 16000000 INFO @ Tue, 16 Jun 2020 09:30:29: 23000000 INFO @ Tue, 16 Jun 2020 09:30:30: 20000000 INFO @ Tue, 16 Jun 2020 09:30:35: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:30:37: 24000000 INFO @ Tue, 16 Jun 2020 09:30:39: 21000000 INFO @ Tue, 16 Jun 2020 09:30:44: 18000000 INFO @ Tue, 16 Jun 2020 09:30:46: 25000000 INFO @ Tue, 16 Jun 2020 09:30:48: 22000000 INFO @ Tue, 16 Jun 2020 09:30:53: 19000000 INFO @ Tue, 16 Jun 2020 09:30:54: 26000000 INFO @ Tue, 16 Jun 2020 09:30:57: 23000000 INFO @ Tue, 16 Jun 2020 09:31:02: 20000000 INFO @ Tue, 16 Jun 2020 09:31:03: 27000000 INFO @ Tue, 16 Jun 2020 09:31:06: 24000000 INFO @ Tue, 16 Jun 2020 09:31:11: 28000000 INFO @ Tue, 16 Jun 2020 09:31:11: 21000000 INFO @ Tue, 16 Jun 2020 09:31:15: 25000000 INFO @ Tue, 16 Jun 2020 09:31:19: 29000000 INFO @ Tue, 16 Jun 2020 09:31:20: 22000000 INFO @ Tue, 16 Jun 2020 09:31:24: 26000000 INFO @ Tue, 16 Jun 2020 09:31:26: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:31:26: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:31:26: #1 total tags in treatment: 29769388 INFO @ Tue, 16 Jun 2020 09:31:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:26: #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 09:31:26: #1 tags after filtering in treatment: 29769388 INFO @ Tue, 16 Jun 2020 09:31:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:28: #2 number of paired peaks: 105 WARNING @ Tue, 16 Jun 2020 09:31:28: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:28: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:31:28: #2 alternative fragment length(s) may be 1,10,29,59,75 bps INFO @ Tue, 16 Jun 2020 09:31:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.05_model.r WARNING @ Tue, 16 Jun 2020 09:31:28: #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 09:31:28: #2 You may need to consider one of the other alternative d(s): 1,10,29,59,75 WARNING @ Tue, 16 Jun 2020 09:31:28: #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 09:31:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:29: 23000000 INFO @ Tue, 16 Jun 2020 09:31:33: 27000000 INFO @ Tue, 16 Jun 2020 09:31:37: 24000000 INFO @ Tue, 16 Jun 2020 09:31:41: 28000000 INFO @ Tue, 16 Jun 2020 09:31:46: 25000000 INFO @ Tue, 16 Jun 2020 09:31:50: 29000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:31:55: 26000000 INFO @ Tue, 16 Jun 2020 09:31:57: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:31:57: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:31:57: #1 total tags in treatment: 29769388 INFO @ Tue, 16 Jun 2020 09:31:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:57: #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 09:31:57: #1 tags after filtering in treatment: 29769388 INFO @ Tue, 16 Jun 2020 09:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:59: #2 number of paired peaks: 105 WARNING @ Tue, 16 Jun 2020 09:31:59: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:59: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:31:59: #2 alternative fragment length(s) may be 1,10,29,59,75 bps INFO @ Tue, 16 Jun 2020 09:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.10_model.r WARNING @ Tue, 16 Jun 2020 09:31:59: #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 09:31:59: #2 You may need to consider one of the other alternative d(s): 1,10,29,59,75 WARNING @ Tue, 16 Jun 2020 09:31:59: #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 09:31:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:03: 27000000 INFO @ Tue, 16 Jun 2020 09:32:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:11: 28000000 INFO @ Tue, 16 Jun 2020 09:32:18: 29000000 INFO @ Tue, 16 Jun 2020 09:32:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:24: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:32:24: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:32:24: #1 total tags in treatment: 29769388 INFO @ Tue, 16 Jun 2020 09:32:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:24: #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 09:32:25: #1 tags after filtering in treatment: 29769388 INFO @ Tue, 16 Jun 2020 09:32:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:27: #2 number of paired peaks: 105 WARNING @ Tue, 16 Jun 2020 09:32:27: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:27: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:32:27: #2 alternative fragment length(s) may be 1,10,29,59,75 bps INFO @ Tue, 16 Jun 2020 09:32:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.20_model.r WARNING @ Tue, 16 Jun 2020 09:32:27: #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 09:32:27: #2 You may need to consider one of the other alternative d(s): 1,10,29,59,75 WARNING @ Tue, 16 Jun 2020 09:32:27: #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 09:32:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965735/SRX2965735.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling