Job ID = 6453257 SRX = SRX110775 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:17:33 prefetch.2.10.7: 1) Downloading 'SRR388357'... 2020-06-21T08:17:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:24:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:24:01 prefetch.2.10.7: 1) 'SRR388357' was downloaded successfully Read 34211332 spots for SRR388357/SRR388357.sra Written 34211332 spots for SRR388357/SRR388357.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: 00:05:48 34211332 reads; of these: 34211332 (100.00%) were unpaired; of these: 7859677 (22.97%) aligned 0 times 23157678 (67.69%) aligned exactly 1 time 3193977 (9.34%) aligned >1 times 77.03% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 10056848 / 26351655 = 0.3816 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 @ Sun, 21 Jun 2020 17:36:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 17:36:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:36:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:36:29: 1000000 INFO @ Sun, 21 Jun 2020 17:36:35: 2000000 INFO @ Sun, 21 Jun 2020 17:36:40: 3000000 INFO @ Sun, 21 Jun 2020 17:36:45: 4000000 INFO @ Sun, 21 Jun 2020 17:36:51: 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 @ Sun, 21 Jun 2020 17:36:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 17:36:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:36:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:36:56: 6000000 INFO @ Sun, 21 Jun 2020 17:36:59: 1000000 INFO @ Sun, 21 Jun 2020 17:37:02: 7000000 INFO @ Sun, 21 Jun 2020 17:37:04: 2000000 INFO @ Sun, 21 Jun 2020 17:37:07: 8000000 INFO @ Sun, 21 Jun 2020 17:37:09: 3000000 INFO @ Sun, 21 Jun 2020 17:37:13: 9000000 INFO @ Sun, 21 Jun 2020 17:37:14: 4000000 INFO @ Sun, 21 Jun 2020 17:37:18: 10000000 INFO @ Sun, 21 Jun 2020 17:37:19: 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 @ Sun, 21 Jun 2020 17:37:23: 6000000 INFO @ Sun, 21 Jun 2020 17:37:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 17:37:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:24: 11000000 INFO @ Sun, 21 Jun 2020 17:37:28: 7000000 INFO @ Sun, 21 Jun 2020 17:37:29: 12000000 INFO @ Sun, 21 Jun 2020 17:37:30: 1000000 INFO @ Sun, 21 Jun 2020 17:37:33: 8000000 INFO @ Sun, 21 Jun 2020 17:37:35: 13000000 INFO @ Sun, 21 Jun 2020 17:37:35: 2000000 INFO @ Sun, 21 Jun 2020 17:37:38: 9000000 INFO @ Sun, 21 Jun 2020 17:37:41: 14000000 INFO @ Sun, 21 Jun 2020 17:37:41: 3000000 INFO @ Sun, 21 Jun 2020 17:37:43: 10000000 INFO @ Sun, 21 Jun 2020 17:37:47: 15000000 INFO @ Sun, 21 Jun 2020 17:37:47: 4000000 INFO @ Sun, 21 Jun 2020 17:37:48: 11000000 INFO @ Sun, 21 Jun 2020 17:37:52: 16000000 INFO @ Sun, 21 Jun 2020 17:37:53: 5000000 INFO @ Sun, 21 Jun 2020 17:37:53: 12000000 INFO @ Sun, 21 Jun 2020 17:37:54: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:37:54: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:37:54: #1 total tags in treatment: 16294807 INFO @ Sun, 21 Jun 2020 17:37:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:37:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:37:55: #1 tags after filtering in treatment: 16294778 INFO @ Sun, 21 Jun 2020 17:37:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:37:55: #1 finished! INFO @ Sun, 21 Jun 2020 17:37:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:37:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:37:56: #2 number of paired peaks: 536 WARNING @ Sun, 21 Jun 2020 17:37:56: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Sun, 21 Jun 2020 17:37:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:37:56: start X-correlation... INFO @ Sun, 21 Jun 2020 17:37:56: end of X-cor INFO @ Sun, 21 Jun 2020 17:37:56: #2 finished! INFO @ Sun, 21 Jun 2020 17:37:56: #2 predicted fragment length is 67 bps INFO @ Sun, 21 Jun 2020 17:37:56: #2 alternative fragment length(s) may be 4,67 bps INFO @ Sun, 21 Jun 2020 17:37:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.05_model.r WARNING @ Sun, 21 Jun 2020 17:37:56: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:37:56: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Sun, 21 Jun 2020 17:37:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:37:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:37:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:37:58: 13000000 INFO @ Sun, 21 Jun 2020 17:37:58: 6000000 INFO @ Sun, 21 Jun 2020 17:38:03: 14000000 INFO @ Sun, 21 Jun 2020 17:38:04: 7000000 INFO @ Sun, 21 Jun 2020 17:38:08: 15000000 INFO @ Sun, 21 Jun 2020 17:38:10: 8000000 INFO @ Sun, 21 Jun 2020 17:38:13: 16000000 INFO @ Sun, 21 Jun 2020 17:38:14: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:38:14: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:38:14: #1 total tags in treatment: 16294807 INFO @ Sun, 21 Jun 2020 17:38:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:38:15: #1 tags after filtering in treatment: 16294778 INFO @ Sun, 21 Jun 2020 17:38:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:15: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:15: 9000000 INFO @ Sun, 21 Jun 2020 17:38:16: #2 number of paired peaks: 536 WARNING @ Sun, 21 Jun 2020 17:38:16: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Sun, 21 Jun 2020 17:38:16: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:16: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:16: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:16: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:16: #2 predicted fragment length is 67 bps INFO @ Sun, 21 Jun 2020 17:38:16: #2 alternative fragment length(s) may be 4,67 bps INFO @ Sun, 21 Jun 2020 17:38:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.10_model.r WARNING @ Sun, 21 Jun 2020 17:38:16: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:38:16: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Sun, 21 Jun 2020 17:38:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:38:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:38:20: 10000000 INFO @ Sun, 21 Jun 2020 17:38:26: 11000000 INFO @ Sun, 21 Jun 2020 17:38:29: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:38:31: 12000000 INFO @ Sun, 21 Jun 2020 17:38:36: 13000000 INFO @ Sun, 21 Jun 2020 17:38:42: 14000000 INFO @ Sun, 21 Jun 2020 17:38:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.05_summits.bed INFO @ Sun, 21 Jun 2020 17:38:46: Done! pass1 - making usageList (473 chroms): 2 millis pass2 - checking and writing primary data (8694 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:38:47: 15000000 INFO @ Sun, 21 Jun 2020 17:38:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:52: 16000000 INFO @ Sun, 21 Jun 2020 17:38:54: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:38:54: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:38:54: #1 total tags in treatment: 16294807 INFO @ Sun, 21 Jun 2020 17:38:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:38:55: #1 tags after filtering in treatment: 16294778 INFO @ Sun, 21 Jun 2020 17:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:55: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:56: #2 number of paired peaks: 536 WARNING @ Sun, 21 Jun 2020 17:38:56: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Sun, 21 Jun 2020 17:38:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:56: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:56: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:56: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:56: #2 predicted fragment length is 67 bps INFO @ Sun, 21 Jun 2020 17:38:56: #2 alternative fragment length(s) may be 4,67 bps INFO @ Sun, 21 Jun 2020 17:38:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.20_model.r WARNING @ Sun, 21 Jun 2020 17:38:56: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:38:56: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Sun, 21 Jun 2020 17:38:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:38:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:39:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.10_summits.bed INFO @ Sun, 21 Jun 2020 17:39:04: Done! pass1 - making usageList (226 chroms): 1 millis pass2 - checking and writing primary data (1848 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:39:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110775/SRX110775.20_summits.bed INFO @ Sun, 21 Jun 2020 17:39:43: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (294 records, 4 fields): 3 millis CompletedMACS2peakCalling