Job ID = 6368072 SRX = SRX466535 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:51:48 prefetch.2.10.7: 1) Downloading 'SRR1163601'... 2020-06-15T23:51:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:04 prefetch.2.10.7: 1) 'SRR1163601' was downloaded successfully Read 30788149 spots for SRR1163601/SRR1163601.sra Written 30788149 spots for SRR1163601/SRR1163601.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: 00:06:01 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169808 (0.55%) aligned 0 times 25275455 (82.09%) aligned exactly 1 time 5342886 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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 8 files... [bam_rmdupse_core] 4711228 / 30618341 = 0.1539 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 09:08:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.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 09:08:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:22: 1000000 INFO @ Tue, 16 Jun 2020 09:08:27: 2000000 INFO @ Tue, 16 Jun 2020 09:08:32: 3000000 INFO @ Tue, 16 Jun 2020 09:08:38: 4000000 INFO @ Tue, 16 Jun 2020 09:08:43: 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 09:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.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 09:08:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:49: 6000000 INFO @ Tue, 16 Jun 2020 09:08:52: 1000000 INFO @ Tue, 16 Jun 2020 09:08:55: 7000000 INFO @ Tue, 16 Jun 2020 09:08:58: 2000000 INFO @ Tue, 16 Jun 2020 09:09:00: 8000000 INFO @ Tue, 16 Jun 2020 09:09:03: 3000000 INFO @ Tue, 16 Jun 2020 09:09:06: 9000000 INFO @ Tue, 16 Jun 2020 09:09:09: 4000000 INFO @ Tue, 16 Jun 2020 09:09:11: 10000000 INFO @ Tue, 16 Jun 2020 09:09:14: 5000000 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 09:09:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.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 09:09:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:17: 11000000 INFO @ Tue, 16 Jun 2020 09:09:20: 6000000 INFO @ Tue, 16 Jun 2020 09:09:23: 12000000 INFO @ Tue, 16 Jun 2020 09:09:23: 1000000 INFO @ Tue, 16 Jun 2020 09:09:26: 7000000 INFO @ Tue, 16 Jun 2020 09:09:28: 13000000 INFO @ Tue, 16 Jun 2020 09:09:29: 2000000 INFO @ Tue, 16 Jun 2020 09:09:31: 8000000 INFO @ Tue, 16 Jun 2020 09:09:34: 14000000 INFO @ Tue, 16 Jun 2020 09:09:35: 3000000 INFO @ Tue, 16 Jun 2020 09:09:37: 9000000 INFO @ Tue, 16 Jun 2020 09:09:39: 15000000 INFO @ Tue, 16 Jun 2020 09:09:42: 4000000 INFO @ Tue, 16 Jun 2020 09:09:43: 10000000 INFO @ Tue, 16 Jun 2020 09:09:45: 16000000 INFO @ Tue, 16 Jun 2020 09:09:48: 5000000 INFO @ Tue, 16 Jun 2020 09:09:49: 11000000 INFO @ Tue, 16 Jun 2020 09:09:51: 17000000 INFO @ Tue, 16 Jun 2020 09:09:54: 6000000 INFO @ Tue, 16 Jun 2020 09:09:55: 12000000 INFO @ Tue, 16 Jun 2020 09:09:56: 18000000 INFO @ Tue, 16 Jun 2020 09:10:01: 7000000 INFO @ Tue, 16 Jun 2020 09:10:01: 13000000 INFO @ Tue, 16 Jun 2020 09:10:02: 19000000 INFO @ Tue, 16 Jun 2020 09:10:07: 8000000 INFO @ Tue, 16 Jun 2020 09:10:07: 14000000 INFO @ Tue, 16 Jun 2020 09:10:07: 20000000 INFO @ Tue, 16 Jun 2020 09:10:13: 21000000 INFO @ Tue, 16 Jun 2020 09:10:13: 9000000 INFO @ Tue, 16 Jun 2020 09:10:14: 15000000 INFO @ Tue, 16 Jun 2020 09:10:19: 22000000 INFO @ Tue, 16 Jun 2020 09:10:20: 16000000 INFO @ Tue, 16 Jun 2020 09:10:20: 10000000 INFO @ Tue, 16 Jun 2020 09:10:24: 23000000 INFO @ Tue, 16 Jun 2020 09:10:26: 17000000 INFO @ Tue, 16 Jun 2020 09:10:26: 11000000 INFO @ Tue, 16 Jun 2020 09:10:30: 24000000 INFO @ Tue, 16 Jun 2020 09:10:32: 18000000 INFO @ Tue, 16 Jun 2020 09:10:32: 12000000 INFO @ Tue, 16 Jun 2020 09:10:35: 25000000 INFO @ Tue, 16 Jun 2020 09:10:38: 19000000 INFO @ Tue, 16 Jun 2020 09:10:39: 13000000 INFO @ Tue, 16 Jun 2020 09:10:41: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:10:41: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:10:41: #1 total tags in treatment: 25907113 INFO @ Tue, 16 Jun 2020 09:10:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:41: #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 09:10:41: #1 tags after filtering in treatment: 25907113 INFO @ Tue, 16 Jun 2020 09:10:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:43: #2 number of paired peaks: 149 WARNING @ Tue, 16 Jun 2020 09:10:43: 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 09:10:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:43: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:10:43: #2 alternative fragment length(s) may be 1,30,491,577,585 bps INFO @ Tue, 16 Jun 2020 09:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.05_model.r WARNING @ Tue, 16 Jun 2020 09:10:43: #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 09:10:43: #2 You may need to consider one of the other alternative d(s): 1,30,491,577,585 WARNING @ Tue, 16 Jun 2020 09:10:43: #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 09:10:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:44: 20000000 INFO @ Tue, 16 Jun 2020 09:10:45: 14000000 INFO @ Tue, 16 Jun 2020 09:10:50: 21000000 INFO @ Tue, 16 Jun 2020 09:10:51: 15000000 INFO @ Tue, 16 Jun 2020 09:10:55: 22000000 INFO @ Tue, 16 Jun 2020 09:10:58: 16000000 INFO @ Tue, 16 Jun 2020 09:11:01: 23000000 INFO @ Tue, 16 Jun 2020 09:11:04: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:11:07: 24000000 INFO @ Tue, 16 Jun 2020 09:11:10: 18000000 INFO @ Tue, 16 Jun 2020 09:11:13: 25000000 INFO @ Tue, 16 Jun 2020 09:11:16: 19000000 INFO @ Tue, 16 Jun 2020 09:11:18: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:11:18: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:11:18: #1 total tags in treatment: 25907113 INFO @ Tue, 16 Jun 2020 09:11:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:18: #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 09:11:19: #1 tags after filtering in treatment: 25907113 INFO @ Tue, 16 Jun 2020 09:11:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:20: #2 number of paired peaks: 149 WARNING @ Tue, 16 Jun 2020 09:11:20: 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 09:11:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:21: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:11:21: #2 alternative fragment length(s) may be 1,30,491,577,585 bps INFO @ Tue, 16 Jun 2020 09:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.10_model.r WARNING @ Tue, 16 Jun 2020 09:11:21: #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 09:11:21: #2 You may need to consider one of the other alternative d(s): 1,30,491,577,585 WARNING @ Tue, 16 Jun 2020 09:11:21: #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 09:11:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:21: 20000000 INFO @ Tue, 16 Jun 2020 09:11:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:27: 21000000 INFO @ Tue, 16 Jun 2020 09:11:32: 22000000 INFO @ Tue, 16 Jun 2020 09:11:38: 23000000 INFO @ Tue, 16 Jun 2020 09:11:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:40: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:43: 24000000 INFO @ Tue, 16 Jun 2020 09:11:48: 25000000 INFO @ Tue, 16 Jun 2020 09:11:53: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:11:53: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:11:53: #1 total tags in treatment: 25907113 INFO @ Tue, 16 Jun 2020 09:11:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:53: #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 09:11:54: #1 tags after filtering in treatment: 25907113 INFO @ Tue, 16 Jun 2020 09:11:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:55: #2 number of paired peaks: 149 WARNING @ Tue, 16 Jun 2020 09:11:55: 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 09:11:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:56: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:11:56: #2 alternative fragment length(s) may be 1,30,491,577,585 bps INFO @ Tue, 16 Jun 2020 09:11:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.20_model.r WARNING @ Tue, 16 Jun 2020 09:11:56: #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 09:11:56: #2 You may need to consider one of the other alternative d(s): 1,30,491,577,585 WARNING @ Tue, 16 Jun 2020 09:11:56: #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 09:11:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466535/SRX466535.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling