Job ID = 6456795 SRX = SRX3981689 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:11:39 prefetch.2.10.7: 1) Downloading 'SRR7050451'... 2020-06-21T11:11:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:12:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:12:33 prefetch.2.10.7: 'SRR7050451' is valid 2020-06-21T11:12:33 prefetch.2.10.7: 1) 'SRR7050451' was downloaded successfully 2020-06-21T11:12:33 prefetch.2.10.7: 'SRR7050451' has 0 unresolved dependencies Read 7041492 spots for SRR7050451/SRR7050451.sra Written 7041492 spots for SRR7050451/SRR7050451.sra 2020-06-21T11:13:06 prefetch.2.10.7: 1) Downloading 'SRR7050452'... 2020-06-21T11:13:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:14:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:14:04 prefetch.2.10.7: 'SRR7050452' is valid 2020-06-21T11:14:04 prefetch.2.10.7: 1) 'SRR7050452' was downloaded successfully 2020-06-21T11:14:04 prefetch.2.10.7: 'SRR7050452' has 0 unresolved dependencies Read 7029892 spots for SRR7050452/SRR7050452.sra Written 7029892 spots for SRR7050452/SRR7050452.sra 2020-06-21T11:14:36 prefetch.2.10.7: 1) Downloading 'SRR7050453'... 2020-06-21T11:14:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:15:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:15:32 prefetch.2.10.7: 'SRR7050453' is valid 2020-06-21T11:15:32 prefetch.2.10.7: 1) 'SRR7050453' was downloaded successfully 2020-06-21T11:15:32 prefetch.2.10.7: 'SRR7050453' has 0 unresolved dependencies Read 7050738 spots for SRR7050453/SRR7050453.sra Written 7050738 spots for SRR7050453/SRR7050453.sra 2020-06-21T11:16:03 prefetch.2.10.7: 1) Downloading 'SRR7050454'... 2020-06-21T11:16:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:16:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:16:45 prefetch.2.10.7: 'SRR7050454' is valid 2020-06-21T11:16:45 prefetch.2.10.7: 1) 'SRR7050454' was downloaded successfully 2020-06-21T11:16:45 prefetch.2.10.7: 'SRR7050454' has 0 unresolved dependencies Read 7093550 spots for SRR7050454/SRR7050454.sra Written 7093550 spots for SRR7050454/SRR7050454.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: 00:07:02 28215672 reads; of these: 28215672 (100.00%) were unpaired; of these: 766557 (2.72%) aligned 0 times 21902584 (77.63%) aligned exactly 1 time 5546531 (19.66%) aligned >1 times 97.28% overall alignment rate Time searching: 00:07:02 Overall time: 00:07:02 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 12 files... [bam_rmdupse_core] 4010809 / 27449115 = 0.1461 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 20:29:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.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 20:29:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:04: 1000000 INFO @ Sun, 21 Jun 2020 20:30:10: 2000000 INFO @ Sun, 21 Jun 2020 20:30:16: 3000000 INFO @ Sun, 21 Jun 2020 20:30:22: 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 @ Sun, 21 Jun 2020 20:30:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.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 20:30:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:28: 5000000 INFO @ Sun, 21 Jun 2020 20:30:34: 1000000 INFO @ Sun, 21 Jun 2020 20:30:34: 6000000 INFO @ Sun, 21 Jun 2020 20:30:41: 7000000 INFO @ Sun, 21 Jun 2020 20:30:41: 2000000 INFO @ Sun, 21 Jun 2020 20:30:47: 8000000 INFO @ Sun, 21 Jun 2020 20:30:47: 3000000 INFO @ Sun, 21 Jun 2020 20:30:53: 9000000 INFO @ Sun, 21 Jun 2020 20:30:54: 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 @ Sun, 21 Jun 2020 20:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.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 20:30:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:31:00: 10000000 INFO @ Sun, 21 Jun 2020 20:31:00: 5000000 INFO @ Sun, 21 Jun 2020 20:31:05: 1000000 INFO @ Sun, 21 Jun 2020 20:31:07: 11000000 INFO @ Sun, 21 Jun 2020 20:31:08: 6000000 INFO @ Sun, 21 Jun 2020 20:31:13: 2000000 INFO @ Sun, 21 Jun 2020 20:31:14: 12000000 INFO @ Sun, 21 Jun 2020 20:31:15: 7000000 INFO @ Sun, 21 Jun 2020 20:31:21: 3000000 INFO @ Sun, 21 Jun 2020 20:31:21: 13000000 INFO @ Sun, 21 Jun 2020 20:31:22: 8000000 INFO @ Sun, 21 Jun 2020 20:31:28: 14000000 INFO @ Sun, 21 Jun 2020 20:31:28: 4000000 INFO @ Sun, 21 Jun 2020 20:31:29: 9000000 INFO @ Sun, 21 Jun 2020 20:31:35: 15000000 INFO @ Sun, 21 Jun 2020 20:31:36: 10000000 INFO @ Sun, 21 Jun 2020 20:31:36: 5000000 INFO @ Sun, 21 Jun 2020 20:31:42: 16000000 INFO @ Sun, 21 Jun 2020 20:31:43: 11000000 INFO @ Sun, 21 Jun 2020 20:31:44: 6000000 INFO @ Sun, 21 Jun 2020 20:31:49: 17000000 INFO @ Sun, 21 Jun 2020 20:31:49: 12000000 INFO @ Sun, 21 Jun 2020 20:31:51: 7000000 INFO @ Sun, 21 Jun 2020 20:31:56: 18000000 INFO @ Sun, 21 Jun 2020 20:31:56: 13000000 INFO @ Sun, 21 Jun 2020 20:31:59: 8000000 INFO @ Sun, 21 Jun 2020 20:32:03: 19000000 INFO @ Sun, 21 Jun 2020 20:32:03: 14000000 INFO @ Sun, 21 Jun 2020 20:32:06: 9000000 INFO @ Sun, 21 Jun 2020 20:32:10: 20000000 INFO @ Sun, 21 Jun 2020 20:32:10: 15000000 INFO @ Sun, 21 Jun 2020 20:32:14: 10000000 INFO @ Sun, 21 Jun 2020 20:32:16: 21000000 INFO @ Sun, 21 Jun 2020 20:32:17: 16000000 INFO @ Sun, 21 Jun 2020 20:32:22: 11000000 INFO @ Sun, 21 Jun 2020 20:32:23: 22000000 INFO @ Sun, 21 Jun 2020 20:32:24: 17000000 INFO @ Sun, 21 Jun 2020 20:32:29: 12000000 INFO @ Sun, 21 Jun 2020 20:32:30: 23000000 INFO @ Sun, 21 Jun 2020 20:32:31: 18000000 INFO @ Sun, 21 Jun 2020 20:32:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:32:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:32:34: #1 total tags in treatment: 23438306 INFO @ Sun, 21 Jun 2020 20:32:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:32:34: #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 20:32:34: #1 tags after filtering in treatment: 23438226 INFO @ Sun, 21 Jun 2020 20:32:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:32:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:32:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:32:36: #2 number of paired peaks: 299 WARNING @ Sun, 21 Jun 2020 20:32:36: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Sun, 21 Jun 2020 20:32:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:32:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:32:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:32:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:32:36: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 20:32:36: #2 alternative fragment length(s) may be 3,61,77 bps INFO @ Sun, 21 Jun 2020 20:32:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.05_model.r WARNING @ Sun, 21 Jun 2020 20:32:36: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:32:36: #2 You may need to consider one of the other alternative d(s): 3,61,77 WARNING @ Sun, 21 Jun 2020 20:32:36: #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 20:32:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:32:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:32:37: 13000000 INFO @ Sun, 21 Jun 2020 20:32:37: 19000000 INFO @ Sun, 21 Jun 2020 20:32:44: 14000000 INFO @ Sun, 21 Jun 2020 20:32:45: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:32:51: 21000000 INFO @ Sun, 21 Jun 2020 20:32:52: 15000000 INFO @ Sun, 21 Jun 2020 20:32:58: 22000000 INFO @ Sun, 21 Jun 2020 20:32:59: 16000000 INFO @ Sun, 21 Jun 2020 20:33:05: 23000000 INFO @ Sun, 21 Jun 2020 20:33:07: 17000000 INFO @ Sun, 21 Jun 2020 20:33:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:33:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:33:08: #1 total tags in treatment: 23438306 INFO @ Sun, 21 Jun 2020 20:33:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:33:08: #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 20:33:09: #1 tags after filtering in treatment: 23438226 INFO @ Sun, 21 Jun 2020 20:33:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:33:09: #1 finished! INFO @ Sun, 21 Jun 2020 20:33:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:33:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:33:10: #2 number of paired peaks: 299 WARNING @ Sun, 21 Jun 2020 20:33:10: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Sun, 21 Jun 2020 20:33:10: start model_add_line... INFO @ Sun, 21 Jun 2020 20:33:11: start X-correlation... INFO @ Sun, 21 Jun 2020 20:33:11: end of X-cor INFO @ Sun, 21 Jun 2020 20:33:11: #2 finished! INFO @ Sun, 21 Jun 2020 20:33:11: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 20:33:11: #2 alternative fragment length(s) may be 3,61,77 bps INFO @ Sun, 21 Jun 2020 20:33:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.10_model.r WARNING @ Sun, 21 Jun 2020 20:33:11: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:33:11: #2 You may need to consider one of the other alternative d(s): 3,61,77 WARNING @ Sun, 21 Jun 2020 20:33:11: #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 20:33:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:33:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:33:14: 18000000 INFO @ Sun, 21 Jun 2020 20:33:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:33:21: 19000000 INFO @ Sun, 21 Jun 2020 20:33:28: 20000000 INFO @ Sun, 21 Jun 2020 20:33:35: 21000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:33:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.05_summits.bed INFO @ Sun, 21 Jun 2020 20:33:38: Done! pass1 - making usageList (439 chroms): 2 millis pass2 - checking and writing primary data (3854 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:33:41: 22000000 INFO @ Sun, 21 Jun 2020 20:33:48: 23000000 INFO @ Sun, 21 Jun 2020 20:33:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:33:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:33:51: #1 total tags in treatment: 23438306 INFO @ Sun, 21 Jun 2020 20:33:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:33:51: #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 20:33:52: #1 tags after filtering in treatment: 23438226 INFO @ Sun, 21 Jun 2020 20:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:33:52: #1 finished! INFO @ Sun, 21 Jun 2020 20:33:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:33:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:33:54: #2 number of paired peaks: 299 WARNING @ Sun, 21 Jun 2020 20:33:54: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Sun, 21 Jun 2020 20:33:54: start model_add_line... INFO @ Sun, 21 Jun 2020 20:33:54: start X-correlation... INFO @ Sun, 21 Jun 2020 20:33:54: end of X-cor INFO @ Sun, 21 Jun 2020 20:33:54: #2 finished! INFO @ Sun, 21 Jun 2020 20:33:54: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 20:33:54: #2 alternative fragment length(s) may be 3,61,77 bps INFO @ Sun, 21 Jun 2020 20:33:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.20_model.r WARNING @ Sun, 21 Jun 2020 20:33:54: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:33:54: #2 You may need to consider one of the other alternative d(s): 3,61,77 WARNING @ Sun, 21 Jun 2020 20:33:54: #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 20:33:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:33:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:34:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:34:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.10_summits.bed INFO @ Sun, 21 Jun 2020 20:34:13: Done! pass1 - making usageList (323 chroms): 1 millis pass2 - checking and writing primary data (1470 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:34:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:34:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:34:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981689/SRX3981689.20_summits.bed INFO @ Sun, 21 Jun 2020 20:34:54: Done! pass1 - making usageList (165 chroms): 1 millis pass2 - checking and writing primary data (526 records, 4 fields): 6 millis CompletedMACS2peakCalling