Job ID = 6456832 SRX = SRX3981719 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:22:09 prefetch.2.10.7: 1) Downloading 'SRR7050569'... 2020-06-21T11:22:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:23:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:23:36 prefetch.2.10.7: 'SRR7050569' is valid 2020-06-21T11:23:36 prefetch.2.10.7: 1) 'SRR7050569' was downloaded successfully 2020-06-21T11:23:36 prefetch.2.10.7: 'SRR7050569' has 0 unresolved dependencies Read 13113957 spots for SRR7050569/SRR7050569.sra Written 13113957 spots for SRR7050569/SRR7050569.sra 2020-06-21T11:24:27 prefetch.2.10.7: 1) Downloading 'SRR7050570'... 2020-06-21T11:24:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:25:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:25:29 prefetch.2.10.7: 'SRR7050570' is valid 2020-06-21T11:25:29 prefetch.2.10.7: 1) 'SRR7050570' was downloaded successfully 2020-06-21T11:25:29 prefetch.2.10.7: 'SRR7050570' has 0 unresolved dependencies Read 13260022 spots for SRR7050570/SRR7050570.sra Written 13260022 spots for SRR7050570/SRR7050570.sra 2020-06-21T11:26:21 prefetch.2.10.7: 1) Downloading 'SRR7050571'... 2020-06-21T11:26:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:27:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:27:20 prefetch.2.10.7: 'SRR7050571' is valid 2020-06-21T11:27:20 prefetch.2.10.7: 1) 'SRR7050571' was downloaded successfully 2020-06-21T11:27:20 prefetch.2.10.7: 'SRR7050571' has 0 unresolved dependencies Read 13320242 spots for SRR7050571/SRR7050571.sra Written 13320242 spots for SRR7050571/SRR7050571.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: 00:11:01 39694221 reads; of these: 39694221 (100.00%) were unpaired; of these: 1239556 (3.12%) aligned 0 times 27570598 (69.46%) aligned exactly 1 time 10884067 (27.42%) aligned >1 times 96.88% overall alignment rate Time searching: 00:11:01 Overall time: 00:11:01 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 16 files... [bam_rmdupse_core] 5631289 / 38454665 = 0.1464 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 20:47:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.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 20:47:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:47:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:47:31: 1000000 INFO @ Sun, 21 Jun 2020 20:47:37: 2000000 INFO @ Sun, 21 Jun 2020 20:47:43: 3000000 INFO @ Sun, 21 Jun 2020 20:47:49: 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 20:47:54: 5000000 INFO @ Sun, 21 Jun 2020 20:47:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.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 20:47:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:47:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:48:01: 6000000 INFO @ Sun, 21 Jun 2020 20:48:02: 1000000 INFO @ Sun, 21 Jun 2020 20:48:07: 7000000 INFO @ Sun, 21 Jun 2020 20:48:08: 2000000 INFO @ Sun, 21 Jun 2020 20:48:14: 8000000 INFO @ Sun, 21 Jun 2020 20:48:15: 3000000 INFO @ Sun, 21 Jun 2020 20:48:20: 9000000 INFO @ Sun, 21 Jun 2020 20:48:21: 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 20:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.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 20:48:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:48:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:48:27: 10000000 INFO @ Sun, 21 Jun 2020 20:48:28: 5000000 INFO @ Sun, 21 Jun 2020 20:48:32: 1000000 INFO @ Sun, 21 Jun 2020 20:48:33: 11000000 INFO @ Sun, 21 Jun 2020 20:48:35: 6000000 INFO @ Sun, 21 Jun 2020 20:48:38: 2000000 INFO @ Sun, 21 Jun 2020 20:48:40: 12000000 INFO @ Sun, 21 Jun 2020 20:48:41: 7000000 INFO @ Sun, 21 Jun 2020 20:48:45: 3000000 INFO @ Sun, 21 Jun 2020 20:48:47: 13000000 INFO @ Sun, 21 Jun 2020 20:48:48: 8000000 INFO @ Sun, 21 Jun 2020 20:48:52: 4000000 INFO @ Sun, 21 Jun 2020 20:48:53: 14000000 INFO @ Sun, 21 Jun 2020 20:48:54: 9000000 INFO @ Sun, 21 Jun 2020 20:48:58: 5000000 INFO @ Sun, 21 Jun 2020 20:49:00: 15000000 INFO @ Sun, 21 Jun 2020 20:49:01: 10000000 INFO @ Sun, 21 Jun 2020 20:49:05: 6000000 INFO @ Sun, 21 Jun 2020 20:49:07: 16000000 INFO @ Sun, 21 Jun 2020 20:49:07: 11000000 INFO @ Sun, 21 Jun 2020 20:49:11: 7000000 INFO @ Sun, 21 Jun 2020 20:49:13: 17000000 INFO @ Sun, 21 Jun 2020 20:49:14: 12000000 INFO @ Sun, 21 Jun 2020 20:49:18: 8000000 INFO @ Sun, 21 Jun 2020 20:49:20: 18000000 INFO @ Sun, 21 Jun 2020 20:49:21: 13000000 INFO @ Sun, 21 Jun 2020 20:49:25: 9000000 INFO @ Sun, 21 Jun 2020 20:49:27: 19000000 INFO @ Sun, 21 Jun 2020 20:49:27: 14000000 INFO @ Sun, 21 Jun 2020 20:49:31: 10000000 INFO @ Sun, 21 Jun 2020 20:49:33: 20000000 INFO @ Sun, 21 Jun 2020 20:49:34: 15000000 INFO @ Sun, 21 Jun 2020 20:49:38: 11000000 INFO @ Sun, 21 Jun 2020 20:49:41: 21000000 INFO @ Sun, 21 Jun 2020 20:49:41: 16000000 INFO @ Sun, 21 Jun 2020 20:49:44: 12000000 INFO @ Sun, 21 Jun 2020 20:49:47: 17000000 INFO @ Sun, 21 Jun 2020 20:49:48: 22000000 INFO @ Sun, 21 Jun 2020 20:49:51: 13000000 INFO @ Sun, 21 Jun 2020 20:49:54: 18000000 INFO @ Sun, 21 Jun 2020 20:49:55: 23000000 INFO @ Sun, 21 Jun 2020 20:49:58: 14000000 INFO @ Sun, 21 Jun 2020 20:50:00: 19000000 INFO @ Sun, 21 Jun 2020 20:50:02: 24000000 INFO @ Sun, 21 Jun 2020 20:50:04: 15000000 INFO @ Sun, 21 Jun 2020 20:50:07: 20000000 INFO @ Sun, 21 Jun 2020 20:50:08: 25000000 INFO @ Sun, 21 Jun 2020 20:50:11: 16000000 INFO @ Sun, 21 Jun 2020 20:50:14: 21000000 INFO @ Sun, 21 Jun 2020 20:50:15: 26000000 INFO @ Sun, 21 Jun 2020 20:50:17: 17000000 INFO @ Sun, 21 Jun 2020 20:50:21: 27000000 INFO @ Sun, 21 Jun 2020 20:50:21: 22000000 INFO @ Sun, 21 Jun 2020 20:50:23: 18000000 INFO @ Sun, 21 Jun 2020 20:50:28: 23000000 INFO @ Sun, 21 Jun 2020 20:50:28: 28000000 INFO @ Sun, 21 Jun 2020 20:50:30: 19000000 INFO @ Sun, 21 Jun 2020 20:50:35: 24000000 INFO @ Sun, 21 Jun 2020 20:50:35: 29000000 INFO @ Sun, 21 Jun 2020 20:50:36: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:50:41: 25000000 INFO @ Sun, 21 Jun 2020 20:50:42: 30000000 INFO @ Sun, 21 Jun 2020 20:50:44: 21000000 INFO @ Sun, 21 Jun 2020 20:50:48: 26000000 INFO @ Sun, 21 Jun 2020 20:50:49: 31000000 INFO @ Sun, 21 Jun 2020 20:50:51: 22000000 INFO @ Sun, 21 Jun 2020 20:50:54: 27000000 INFO @ Sun, 21 Jun 2020 20:50:55: 32000000 INFO @ Sun, 21 Jun 2020 20:50:58: 23000000 INFO @ Sun, 21 Jun 2020 20:51:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:51:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:51:01: #1 total tags in treatment: 32823376 INFO @ Sun, 21 Jun 2020 20:51:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:01: #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 20:51:01: 28000000 INFO @ Sun, 21 Jun 2020 20:51:02: #1 tags after filtering in treatment: 32823321 INFO @ Sun, 21 Jun 2020 20:51:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:02: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:04: #2 number of paired peaks: 265 WARNING @ Sun, 21 Jun 2020 20:51:04: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Sun, 21 Jun 2020 20:51:04: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:04: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:04: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:04: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:04: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:51:04: #2 alternative fragment length(s) may be 1,53,596 bps INFO @ Sun, 21 Jun 2020 20:51:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.05_model.r WARNING @ Sun, 21 Jun 2020 20:51:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:51:04: #2 You may need to consider one of the other alternative d(s): 1,53,596 WARNING @ Sun, 21 Jun 2020 20:51:04: #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 20:51:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:51:04: 24000000 INFO @ Sun, 21 Jun 2020 20:51:08: 29000000 INFO @ Sun, 21 Jun 2020 20:51:11: 25000000 INFO @ Sun, 21 Jun 2020 20:51:15: 30000000 INFO @ Sun, 21 Jun 2020 20:51:17: 26000000 INFO @ Sun, 21 Jun 2020 20:51:21: 31000000 INFO @ Sun, 21 Jun 2020 20:51:23: 27000000 INFO @ Sun, 21 Jun 2020 20:51:28: 32000000 INFO @ Sun, 21 Jun 2020 20:51:30: 28000000 INFO @ Sun, 21 Jun 2020 20:51:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:51:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:51:33: #1 total tags in treatment: 32823376 INFO @ Sun, 21 Jun 2020 20:51:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:33: #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 20:51:34: #1 tags after filtering in treatment: 32823321 INFO @ Sun, 21 Jun 2020 20:51:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:36: #2 number of paired peaks: 265 WARNING @ Sun, 21 Jun 2020 20:51:36: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Sun, 21 Jun 2020 20:51:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:36: 29000000 INFO @ Sun, 21 Jun 2020 20:51:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:37: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:51:37: #2 alternative fragment length(s) may be 1,53,596 bps INFO @ Sun, 21 Jun 2020 20:51:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.10_model.r WARNING @ Sun, 21 Jun 2020 20:51:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:51:37: #2 You may need to consider one of the other alternative d(s): 1,53,596 WARNING @ Sun, 21 Jun 2020 20:51:37: #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 20:51:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:51:43: 30000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:51:49: 31000000 INFO @ Sun, 21 Jun 2020 20:51:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:51:55: 32000000 INFO @ Sun, 21 Jun 2020 20:52:00: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:52:00: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:52:00: #1 total tags in treatment: 32823376 INFO @ Sun, 21 Jun 2020 20:52:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:00: #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 20:52:01: #1 tags after filtering in treatment: 32823321 INFO @ Sun, 21 Jun 2020 20:52:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:01: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:03: #2 number of paired peaks: 265 WARNING @ Sun, 21 Jun 2020 20:52:03: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Sun, 21 Jun 2020 20:52:03: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:03: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:03: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:03: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:03: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:52:03: #2 alternative fragment length(s) may be 1,53,596 bps INFO @ Sun, 21 Jun 2020 20:52:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.20_model.r WARNING @ Sun, 21 Jun 2020 20:52:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:52:03: #2 You may need to consider one of the other alternative d(s): 1,53,596 WARNING @ Sun, 21 Jun 2020 20:52:03: #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 20:52:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:52:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.05_summits.bed INFO @ Sun, 21 Jun 2020 20:52:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:52:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:52:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.10_summits.bed INFO @ Sun, 21 Jun 2020 20:52:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:52:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:53:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981719/SRX3981719.20_summits.bed INFO @ Sun, 21 Jun 2020 20:53:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling