Job ID = 6367606 SRX = SRX331362 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:30:05 prefetch.2.10.7: 1) Downloading 'SRR947599'... 2020-06-15T23:30:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:13 prefetch.2.10.7: 'SRR947599' is valid 2020-06-15T23:32:13 prefetch.2.10.7: 1) 'SRR947599' was downloaded successfully Read 13338445 spots for SRR947599/SRR947599.sra Written 13338445 spots for SRR947599/SRR947599.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: 00:02:31 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 88329 (0.66%) aligned 0 times 10992845 (82.41%) aligned exactly 1 time 2257271 (16.92%) aligned >1 times 99.34% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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_rmdupse_core] 2114485 / 13250116 = 0.1596 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 08:38:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.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 08:38:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:44: 1000000 INFO @ Tue, 16 Jun 2020 08:38:49: 2000000 INFO @ Tue, 16 Jun 2020 08:38:54: 3000000 INFO @ Tue, 16 Jun 2020 08:38:59: 4000000 INFO @ Tue, 16 Jun 2020 08:39:05: 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 08:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.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 08:39:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:10: 6000000 INFO @ Tue, 16 Jun 2020 08:39:15: 1000000 INFO @ Tue, 16 Jun 2020 08:39:16: 7000000 INFO @ Tue, 16 Jun 2020 08:39:22: 2000000 INFO @ Tue, 16 Jun 2020 08:39:23: 8000000 INFO @ Tue, 16 Jun 2020 08:39:29: 3000000 INFO @ Tue, 16 Jun 2020 08:39:29: 9000000 INFO @ Tue, 16 Jun 2020 08:39:35: 10000000 INFO @ Tue, 16 Jun 2020 08:39:35: 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 08:39:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.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 08:39:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:41: 11000000 INFO @ Tue, 16 Jun 2020 08:39:42: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:39:42: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:39:42: #1 total tags in treatment: 11135631 INFO @ Tue, 16 Jun 2020 08:39:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:42: #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 08:39:42: 5000000 INFO @ Tue, 16 Jun 2020 08:39:42: #1 tags after filtering in treatment: 11135631 INFO @ Tue, 16 Jun 2020 08:39:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:43: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 08:39:43: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:43: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 08:39:43: #2 alternative fragment length(s) may be 2,40,560,598 bps INFO @ Tue, 16 Jun 2020 08:39:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.05_model.r WARNING @ Tue, 16 Jun 2020 08:39:43: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:39:43: #2 You may need to consider one of the other alternative d(s): 2,40,560,598 WARNING @ Tue, 16 Jun 2020 08:39:43: #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 08:39:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:45: 1000000 INFO @ Tue, 16 Jun 2020 08:39:49: 6000000 INFO @ Tue, 16 Jun 2020 08:39:52: 2000000 INFO @ Tue, 16 Jun 2020 08:39:56: 7000000 INFO @ Tue, 16 Jun 2020 08:39:59: 3000000 INFO @ Tue, 16 Jun 2020 08:40:03: 8000000 INFO @ Tue, 16 Jun 2020 08:40:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:05: 4000000 INFO @ Tue, 16 Jun 2020 08:40:10: 9000000 INFO @ Tue, 16 Jun 2020 08:40:12: 5000000 INFO @ Tue, 16 Jun 2020 08:40:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.05_summits.bed INFO @ Tue, 16 Jun 2020 08:40:16: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (935 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:17: 10000000 INFO @ Tue, 16 Jun 2020 08:40:19: 6000000 INFO @ Tue, 16 Jun 2020 08:40:24: 11000000 INFO @ Tue, 16 Jun 2020 08:40:25: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:40:25: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:40:25: #1 total tags in treatment: 11135631 INFO @ Tue, 16 Jun 2020 08:40:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:25: #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 08:40:25: #1 tags after filtering in treatment: 11135631 INFO @ Tue, 16 Jun 2020 08:40:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:26: 7000000 INFO @ Tue, 16 Jun 2020 08:40:26: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 08:40:26: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:26: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 08:40:26: #2 alternative fragment length(s) may be 2,40,560,598 bps INFO @ Tue, 16 Jun 2020 08:40:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.10_model.r WARNING @ Tue, 16 Jun 2020 08:40:26: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:26: #2 You may need to consider one of the other alternative d(s): 2,40,560,598 WARNING @ Tue, 16 Jun 2020 08:40:26: #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 08:40:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:32: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:40:39: 9000000 INFO @ Tue, 16 Jun 2020 08:40:45: 10000000 INFO @ Tue, 16 Jun 2020 08:40:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:51: 11000000 INFO @ Tue, 16 Jun 2020 08:40:52: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:40:52: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:40:52: #1 total tags in treatment: 11135631 INFO @ Tue, 16 Jun 2020 08:40:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:52: #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 08:40:52: #1 tags after filtering in treatment: 11135631 INFO @ Tue, 16 Jun 2020 08:40:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:53: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 08:40:53: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:53: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 08:40:53: #2 alternative fragment length(s) may be 2,40,560,598 bps INFO @ Tue, 16 Jun 2020 08:40:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.20_model.r WARNING @ Tue, 16 Jun 2020 08:40:53: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:53: #2 You may need to consider one of the other alternative d(s): 2,40,560,598 WARNING @ Tue, 16 Jun 2020 08:40:53: #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 08:40:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.10_summits.bed INFO @ Tue, 16 Jun 2020 08:40:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:41:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331362/SRX331362.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (126 records, 4 fields): 1 millis CompletedMACS2peakCalling