Job ID = 6509135 SRX = SRX681817 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:14:43 prefetch.2.10.7: 1) Downloading 'SRR1552286'... 2020-06-26T15:14:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:31:23 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:31:23 prefetch.2.10.7: 1) 'SRR1552286' was downloaded successfully Read 195883261 spots for SRR1552286/SRR1552286.sra Written 195883261 spots for SRR1552286/SRR1552286.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:44:53 195883261 reads; of these: 195883261 (100.00%) were unpaired; of these: 29342115 (14.98%) aligned 0 times 149906917 (76.53%) aligned exactly 1 time 16634229 (8.49%) aligned >1 times 85.02% overall alignment rate Time searching: 00:44:54 Overall time: 00:44:54 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 68 files... [bam_rmdupse_core] 127219380 / 166541146 = 0.7639 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 @ Sat, 27 Jun 2020 01:53:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.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 @ Sat, 27 Jun 2020 01:53:31: #1 read tag files... INFO @ Sat, 27 Jun 2020 01:53:31: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 01:53:37: 1000000 INFO @ Sat, 27 Jun 2020 01:53:43: 2000000 INFO @ Sat, 27 Jun 2020 01:53:49: 3000000 INFO @ Sat, 27 Jun 2020 01:53:55: 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 @ Sat, 27 Jun 2020 01:54:01: 5000000 INFO @ Sat, 27 Jun 2020 01:54:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.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 @ Sat, 27 Jun 2020 01:54:01: #1 read tag files... INFO @ Sat, 27 Jun 2020 01:54:01: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 01:54:07: 6000000 INFO @ Sat, 27 Jun 2020 01:54:08: 1000000 INFO @ Sat, 27 Jun 2020 01:54:13: 7000000 INFO @ Sat, 27 Jun 2020 01:54:15: 2000000 INFO @ Sat, 27 Jun 2020 01:54:20: 8000000 INFO @ Sat, 27 Jun 2020 01:54:22: 3000000 INFO @ Sat, 27 Jun 2020 01:54:26: 9000000 INFO @ Sat, 27 Jun 2020 01:54:28: 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 @ Sat, 27 Jun 2020 01:54:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.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 @ Sat, 27 Jun 2020 01:54:31: #1 read tag files... INFO @ Sat, 27 Jun 2020 01:54:31: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 01:54:32: 10000000 INFO @ Sat, 27 Jun 2020 01:54:35: 5000000 INFO @ Sat, 27 Jun 2020 01:54:38: 1000000 INFO @ Sat, 27 Jun 2020 01:54:39: 11000000 INFO @ Sat, 27 Jun 2020 01:54:42: 6000000 INFO @ Sat, 27 Jun 2020 01:54:45: 12000000 INFO @ Sat, 27 Jun 2020 01:54:45: 2000000 INFO @ Sat, 27 Jun 2020 01:54:49: 7000000 INFO @ Sat, 27 Jun 2020 01:54:52: 13000000 INFO @ Sat, 27 Jun 2020 01:54:52: 3000000 INFO @ Sat, 27 Jun 2020 01:54:56: 8000000 INFO @ Sat, 27 Jun 2020 01:54:58: 14000000 INFO @ Sat, 27 Jun 2020 01:54:59: 4000000 INFO @ Sat, 27 Jun 2020 01:55:03: 9000000 INFO @ Sat, 27 Jun 2020 01:55:04: 15000000 INFO @ Sat, 27 Jun 2020 01:55:05: 5000000 INFO @ Sat, 27 Jun 2020 01:55:09: 10000000 INFO @ Sat, 27 Jun 2020 01:55:11: 16000000 INFO @ Sat, 27 Jun 2020 01:55:12: 6000000 INFO @ Sat, 27 Jun 2020 01:55:16: 11000000 INFO @ Sat, 27 Jun 2020 01:55:17: 17000000 INFO @ Sat, 27 Jun 2020 01:55:18: 7000000 INFO @ Sat, 27 Jun 2020 01:55:23: 12000000 INFO @ Sat, 27 Jun 2020 01:55:24: 18000000 INFO @ Sat, 27 Jun 2020 01:55:25: 8000000 INFO @ Sat, 27 Jun 2020 01:55:30: 13000000 INFO @ Sat, 27 Jun 2020 01:55:30: 19000000 INFO @ Sat, 27 Jun 2020 01:55:32: 9000000 INFO @ Sat, 27 Jun 2020 01:55:36: 20000000 INFO @ Sat, 27 Jun 2020 01:55:37: 14000000 INFO @ Sat, 27 Jun 2020 01:55:39: 10000000 INFO @ Sat, 27 Jun 2020 01:55:43: 21000000 INFO @ Sat, 27 Jun 2020 01:55:43: 15000000 INFO @ Sat, 27 Jun 2020 01:55:46: 11000000 INFO @ Sat, 27 Jun 2020 01:55:49: 22000000 INFO @ Sat, 27 Jun 2020 01:55:50: 16000000 INFO @ Sat, 27 Jun 2020 01:55:53: 12000000 INFO @ Sat, 27 Jun 2020 01:55:56: 23000000 INFO @ Sat, 27 Jun 2020 01:55:57: 17000000 INFO @ Sat, 27 Jun 2020 01:56:00: 13000000 INFO @ Sat, 27 Jun 2020 01:56:02: 24000000 INFO @ Sat, 27 Jun 2020 01:56:04: 18000000 INFO @ Sat, 27 Jun 2020 01:56:07: 14000000 INFO @ Sat, 27 Jun 2020 01:56:08: 25000000 INFO @ Sat, 27 Jun 2020 01:56:10: 19000000 INFO @ Sat, 27 Jun 2020 01:56:14: 15000000 INFO @ Sat, 27 Jun 2020 01:56:15: 26000000 INFO @ Sat, 27 Jun 2020 01:56:17: 20000000 INFO @ Sat, 27 Jun 2020 01:56:21: 16000000 INFO @ Sat, 27 Jun 2020 01:56:21: 27000000 INFO @ Sat, 27 Jun 2020 01:56:24: 21000000 INFO @ Sat, 27 Jun 2020 01:56:27: 28000000 INFO @ Sat, 27 Jun 2020 01:56:28: 17000000 INFO @ Sat, 27 Jun 2020 01:56:31: 22000000 INFO @ Sat, 27 Jun 2020 01:56:34: 29000000 INFO @ Sat, 27 Jun 2020 01:56:35: 18000000 INFO @ Sat, 27 Jun 2020 01:56:38: 23000000 INFO @ Sat, 27 Jun 2020 01:56:40: 30000000 INFO @ Sat, 27 Jun 2020 01:56:42: 19000000 INFO @ Sat, 27 Jun 2020 01:56:45: 24000000 INFO @ Sat, 27 Jun 2020 01:56:46: 31000000 INFO @ Sat, 27 Jun 2020 01:56:49: 20000000 INFO @ Sat, 27 Jun 2020 01:56:51: 25000000 INFO @ Sat, 27 Jun 2020 01:56:53: 32000000 INFO @ Sat, 27 Jun 2020 01:56:57: 21000000 INFO @ Sat, 27 Jun 2020 01:56:58: 26000000 INFO @ Sat, 27 Jun 2020 01:56:59: 33000000 INFO @ Sat, 27 Jun 2020 01:57:04: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 01:57:05: 27000000 INFO @ Sat, 27 Jun 2020 01:57:06: 34000000 INFO @ Sat, 27 Jun 2020 01:57:11: 23000000 INFO @ Sat, 27 Jun 2020 01:57:12: 28000000 INFO @ Sat, 27 Jun 2020 01:57:12: 35000000 INFO @ Sat, 27 Jun 2020 01:57:18: 24000000 INFO @ Sat, 27 Jun 2020 01:57:18: 29000000 INFO @ Sat, 27 Jun 2020 01:57:18: 36000000 INFO @ Sat, 27 Jun 2020 01:57:25: 37000000 INFO @ Sat, 27 Jun 2020 01:57:25: 30000000 INFO @ Sat, 27 Jun 2020 01:57:25: 25000000 INFO @ Sat, 27 Jun 2020 01:57:31: 38000000 INFO @ Sat, 27 Jun 2020 01:57:32: 31000000 INFO @ Sat, 27 Jun 2020 01:57:32: 26000000 INFO @ Sat, 27 Jun 2020 01:57:38: 39000000 INFO @ Sat, 27 Jun 2020 01:57:39: 32000000 INFO @ Sat, 27 Jun 2020 01:57:40: 27000000 INFO @ Sat, 27 Jun 2020 01:57:40: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 01:57:40: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 01:57:40: #1 total tags in treatment: 39321766 INFO @ Sat, 27 Jun 2020 01:57:40: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 01:57:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 01:57:41: #1 tags after filtering in treatment: 39321759 INFO @ Sat, 27 Jun 2020 01:57:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 01:57:41: #1 finished! INFO @ Sat, 27 Jun 2020 01:57:41: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 01:57:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 01:57:43: #2 number of paired peaks: 281 WARNING @ Sat, 27 Jun 2020 01:57:43: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sat, 27 Jun 2020 01:57:43: start model_add_line... INFO @ Sat, 27 Jun 2020 01:57:44: start X-correlation... INFO @ Sat, 27 Jun 2020 01:57:44: end of X-cor INFO @ Sat, 27 Jun 2020 01:57:44: #2 finished! INFO @ Sat, 27 Jun 2020 01:57:44: #2 predicted fragment length is 93 bps INFO @ Sat, 27 Jun 2020 01:57:44: #2 alternative fragment length(s) may be 4,93 bps INFO @ Sat, 27 Jun 2020 01:57:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.05_model.r WARNING @ Sat, 27 Jun 2020 01:57:44: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 01:57:44: #2 You may need to consider one of the other alternative d(s): 4,93 WARNING @ Sat, 27 Jun 2020 01:57:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 01:57:44: #3 Call peaks... INFO @ Sat, 27 Jun 2020 01:57:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 01:57:46: 33000000 INFO @ Sat, 27 Jun 2020 01:57:47: 28000000 INFO @ Sat, 27 Jun 2020 01:57:53: 34000000 INFO @ Sat, 27 Jun 2020 01:57:54: 29000000 INFO @ Sat, 27 Jun 2020 01:58:00: 35000000 INFO @ Sat, 27 Jun 2020 01:58:01: 30000000 INFO @ Sat, 27 Jun 2020 01:58:06: 36000000 INFO @ Sat, 27 Jun 2020 01:58:08: 31000000 INFO @ Sat, 27 Jun 2020 01:58:13: 37000000 BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 01:58:16: 32000000 INFO @ Sat, 27 Jun 2020 01:58:20: 38000000 INFO @ Sat, 27 Jun 2020 01:58:23: 33000000 INFO @ Sat, 27 Jun 2020 01:58:27: 39000000 INFO @ Sat, 27 Jun 2020 01:58:30: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 01:58:30: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 01:58:30: #1 total tags in treatment: 39321766 INFO @ Sat, 27 Jun 2020 01:58:30: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 01:58:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 01:58:30: 34000000 INFO @ Sat, 27 Jun 2020 01:58:31: #1 tags after filtering in treatment: 39321759 INFO @ Sat, 27 Jun 2020 01:58:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 01:58:31: #1 finished! INFO @ Sat, 27 Jun 2020 01:58:31: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 01:58:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 01:58:33: #2 number of paired peaks: 281 WARNING @ Sat, 27 Jun 2020 01:58:33: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sat, 27 Jun 2020 01:58:33: start model_add_line... INFO @ Sat, 27 Jun 2020 01:58:33: start X-correlation... INFO @ Sat, 27 Jun 2020 01:58:33: end of X-cor INFO @ Sat, 27 Jun 2020 01:58:33: #2 finished! INFO @ Sat, 27 Jun 2020 01:58:33: #2 predicted fragment length is 93 bps INFO @ Sat, 27 Jun 2020 01:58:33: #2 alternative fragment length(s) may be 4,93 bps INFO @ Sat, 27 Jun 2020 01:58:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.10_model.r WARNING @ Sat, 27 Jun 2020 01:58:33: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 01:58:33: #2 You may need to consider one of the other alternative d(s): 4,93 WARNING @ Sat, 27 Jun 2020 01:58:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 01:58:33: #3 Call peaks... INFO @ Sat, 27 Jun 2020 01:58:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 01:58:36: 35000000 INFO @ Sat, 27 Jun 2020 01:58:43: 36000000 INFO @ Sat, 27 Jun 2020 01:58:47: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 01:58:50: 37000000 INFO @ Sat, 27 Jun 2020 01:58:57: 38000000 INFO @ Sat, 27 Jun 2020 01:59:04: 39000000 INFO @ Sat, 27 Jun 2020 01:59:06: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 01:59:06: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 01:59:06: #1 total tags in treatment: 39321766 INFO @ Sat, 27 Jun 2020 01:59:06: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 01:59:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 01:59:07: #1 tags after filtering in treatment: 39321759 INFO @ Sat, 27 Jun 2020 01:59:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 01:59:07: #1 finished! INFO @ Sat, 27 Jun 2020 01:59:07: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 01:59:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 01:59:09: #2 number of paired peaks: 281 WARNING @ Sat, 27 Jun 2020 01:59:09: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sat, 27 Jun 2020 01:59:09: start model_add_line... INFO @ Sat, 27 Jun 2020 01:59:10: start X-correlation... INFO @ Sat, 27 Jun 2020 01:59:10: end of X-cor INFO @ Sat, 27 Jun 2020 01:59:10: #2 finished! INFO @ Sat, 27 Jun 2020 01:59:10: #2 predicted fragment length is 93 bps INFO @ Sat, 27 Jun 2020 01:59:10: #2 alternative fragment length(s) may be 4,93 bps INFO @ Sat, 27 Jun 2020 01:59:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.20_model.r WARNING @ Sat, 27 Jun 2020 01:59:10: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 01:59:10: #2 You may need to consider one of the other alternative d(s): 4,93 WARNING @ Sat, 27 Jun 2020 01:59:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 01:59:10: #3 Call peaks... INFO @ Sat, 27 Jun 2020 01:59:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 01:59:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.05_peaks.xls INFO @ Sat, 27 Jun 2020 01:59:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 01:59:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.05_summits.bed INFO @ Sat, 27 Jun 2020 01:59:19: Done! pass1 - making usageList (854 chroms): 4 millis pass2 - checking and writing primary data (23858 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 01:59:36: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 02:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.10_peaks.xls INFO @ Sat, 27 Jun 2020 02:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 02:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.10_summits.bed INFO @ Sat, 27 Jun 2020 02:00:08: Done! pass1 - making usageList (658 chroms): 3 millis pass2 - checking and writing primary data (14717 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 02:00:17: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 02:00:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.20_peaks.xls INFO @ Sat, 27 Jun 2020 02:00:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 02:00:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX681817/SRX681817.20_summits.bed INFO @ Sat, 27 Jun 2020 02:00:51: Done! pass1 - making usageList (497 chroms): 2 millis pass2 - checking and writing primary data (7637 records, 4 fields): 18 millis CompletedMACS2peakCalling