Job ID = 6366545 SRX = SRX1844113 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:49:22 prefetch.2.10.7: 1) Downloading 'SRR3665605'... 2020-06-15T22:49:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:51:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:51:12 prefetch.2.10.7: 1) 'SRR3665605' was downloaded successfully Read 22258098 spots for SRR3665605/SRR3665605.sra Written 22258098 spots for SRR3665605/SRR3665605.sra 2020-06-15T22:52:30 prefetch.2.10.7: 1) Downloading 'SRR3665606'... 2020-06-15T22:52:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:24 prefetch.2.10.7: 1) 'SRR3665606' was downloaded successfully Read 21894547 spots for SRR3665606/SRR3665606.sra Written 21894547 spots for SRR3665606/SRR3665606.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: 00:09:07 44152645 reads; of these: 44152645 (100.00%) were unpaired; of these: 11253550 (25.49%) aligned 0 times 28563410 (64.69%) aligned exactly 1 time 4335685 (9.82%) aligned >1 times 74.51% overall alignment rate Time searching: 00:09:07 Overall time: 00:09:07 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] 18962997 / 32899095 = 0.5764 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 08:11:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.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 08:11:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:02: 1000000 INFO @ Tue, 16 Jun 2020 08:12:08: 2000000 INFO @ Tue, 16 Jun 2020 08:12:14: 3000000 INFO @ Tue, 16 Jun 2020 08:12:20: 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 08:12:26: 5000000 INFO @ Tue, 16 Jun 2020 08:12:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.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 08:12:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:32: 6000000 INFO @ Tue, 16 Jun 2020 08:12:34: 1000000 INFO @ Tue, 16 Jun 2020 08:12:38: 7000000 INFO @ Tue, 16 Jun 2020 08:12:40: 2000000 INFO @ Tue, 16 Jun 2020 08:12:45: 8000000 INFO @ Tue, 16 Jun 2020 08:12:46: 3000000 INFO @ Tue, 16 Jun 2020 08:12:51: 9000000 INFO @ Tue, 16 Jun 2020 08:12:52: 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 08:12:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.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 08:12:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:58: 10000000 INFO @ Tue, 16 Jun 2020 08:12:59: 5000000 INFO @ Tue, 16 Jun 2020 08:13:04: 1000000 INFO @ Tue, 16 Jun 2020 08:13:04: 11000000 INFO @ Tue, 16 Jun 2020 08:13:06: 6000000 INFO @ Tue, 16 Jun 2020 08:13:11: 2000000 INFO @ Tue, 16 Jun 2020 08:13:11: 12000000 INFO @ Tue, 16 Jun 2020 08:13:12: 7000000 INFO @ Tue, 16 Jun 2020 08:13:18: 13000000 INFO @ Tue, 16 Jun 2020 08:13:18: 3000000 INFO @ Tue, 16 Jun 2020 08:13:19: 8000000 INFO @ Tue, 16 Jun 2020 08:13:24: #1 tag size is determined as 45 bps INFO @ Tue, 16 Jun 2020 08:13:24: #1 tag size = 45 INFO @ Tue, 16 Jun 2020 08:13:24: #1 total tags in treatment: 13936098 INFO @ Tue, 16 Jun 2020 08:13:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:24: #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 08:13:24: #1 tags after filtering in treatment: 13936098 INFO @ Tue, 16 Jun 2020 08:13:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:25: 4000000 INFO @ Tue, 16 Jun 2020 08:13:25: #2 number of paired peaks: 127 WARNING @ Tue, 16 Jun 2020 08:13:25: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:25: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:13:25: #2 alternative fragment length(s) may be 2,33,63,86,578 bps INFO @ Tue, 16 Jun 2020 08:13:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.05_model.r WARNING @ Tue, 16 Jun 2020 08:13:25: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:13:25: #2 You may need to consider one of the other alternative d(s): 2,33,63,86,578 WARNING @ Tue, 16 Jun 2020 08:13:25: #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 08:13:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:26: 9000000 INFO @ Tue, 16 Jun 2020 08:13:32: 5000000 INFO @ Tue, 16 Jun 2020 08:13:32: 10000000 INFO @ Tue, 16 Jun 2020 08:13:39: 6000000 INFO @ Tue, 16 Jun 2020 08:13:39: 11000000 INFO @ Tue, 16 Jun 2020 08:13:46: 12000000 INFO @ Tue, 16 Jun 2020 08:13:46: 7000000 INFO @ Tue, 16 Jun 2020 08:13:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:52: 13000000 INFO @ Tue, 16 Jun 2020 08:13:53: 8000000 INFO @ Tue, 16 Jun 2020 08:13:59: #1 tag size is determined as 45 bps INFO @ Tue, 16 Jun 2020 08:13:59: #1 tag size = 45 INFO @ Tue, 16 Jun 2020 08:13:59: #1 total tags in treatment: 13936098 INFO @ Tue, 16 Jun 2020 08:13:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:59: #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 08:13:59: #1 tags after filtering in treatment: 13936098 INFO @ Tue, 16 Jun 2020 08:13:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:00: #2 number of paired peaks: 127 WARNING @ Tue, 16 Jun 2020 08:14:00: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:00: 9000000 INFO @ Tue, 16 Jun 2020 08:14:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:00: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:14:00: #2 alternative fragment length(s) may be 2,33,63,86,578 bps INFO @ Tue, 16 Jun 2020 08:14:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.10_model.r WARNING @ Tue, 16 Jun 2020 08:14:00: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:00: #2 You may need to consider one of the other alternative d(s): 2,33,63,86,578 WARNING @ Tue, 16 Jun 2020 08:14:00: #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 08:14:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.05_summits.bed INFO @ Tue, 16 Jun 2020 08:14:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:07: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:14: 11000000 INFO @ Tue, 16 Jun 2020 08:14:20: 12000000 INFO @ Tue, 16 Jun 2020 08:14:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:27: 13000000 INFO @ Tue, 16 Jun 2020 08:14:34: #1 tag size is determined as 45 bps INFO @ Tue, 16 Jun 2020 08:14:34: #1 tag size = 45 INFO @ Tue, 16 Jun 2020 08:14:34: #1 total tags in treatment: 13936098 INFO @ Tue, 16 Jun 2020 08:14:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:34: #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 08:14:34: #1 tags after filtering in treatment: 13936098 INFO @ Tue, 16 Jun 2020 08:14:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:35: #2 number of paired peaks: 127 WARNING @ Tue, 16 Jun 2020 08:14:35: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:35: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:14:35: #2 alternative fragment length(s) may be 2,33,63,86,578 bps INFO @ Tue, 16 Jun 2020 08:14:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.20_model.r WARNING @ Tue, 16 Jun 2020 08:14:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:35: #2 You may need to consider one of the other alternative d(s): 2,33,63,86,578 WARNING @ Tue, 16 Jun 2020 08:14:35: #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 08:14:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.10_summits.bed INFO @ Tue, 16 Jun 2020 08:14:38: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:15:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1844113/SRX1844113.20_summits.bed INFO @ Tue, 16 Jun 2020 08:15:13: Done! pass1 - making usageList (0 chroms): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling