Job ID = 6454508 SRX = SRX2172426 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:21:29 prefetch.2.10.7: 1) Downloading 'SRR4252437'... 2020-06-21T09:21:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:25:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:25:40 prefetch.2.10.7: 1) 'SRR4252437' was downloaded successfully 2020-06-21T09:25:40 prefetch.2.10.7: 'SRR4252437' has 0 unresolved dependencies Read 44189125 spots for SRR4252437/SRR4252437.sra Written 44189125 spots for SRR4252437/SRR4252437.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: 00:11:26 44189125 reads; of these: 44189125 (100.00%) were unpaired; of these: 1845951 (4.18%) aligned 0 times 32487306 (73.52%) aligned exactly 1 time 9855868 (22.30%) aligned >1 times 95.82% overall alignment rate Time searching: 00:11:26 Overall time: 00:11:26 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 20 files... [bam_rmdupse_core] 6500088 / 42343174 = 0.1535 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 18:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.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 18:50:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:16: 1000000 INFO @ Sun, 21 Jun 2020 18:50:23: 2000000 INFO @ Sun, 21 Jun 2020 18:50:30: 3000000 INFO @ Sun, 21 Jun 2020 18:50:36: 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 18:50:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.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 18:50:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:43: 5000000 INFO @ Sun, 21 Jun 2020 18:50:46: 1000000 INFO @ Sun, 21 Jun 2020 18:50:50: 6000000 INFO @ Sun, 21 Jun 2020 18:50:52: 2000000 INFO @ Sun, 21 Jun 2020 18:50:57: 7000000 INFO @ Sun, 21 Jun 2020 18:50:57: 3000000 INFO @ Sun, 21 Jun 2020 18:51:03: 4000000 INFO @ Sun, 21 Jun 2020 18:51:03: 8000000 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 18:51:09: 5000000 INFO @ Sun, 21 Jun 2020 18:51:10: 9000000 INFO @ Sun, 21 Jun 2020 18:51:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.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 18:51:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:15: 6000000 INFO @ Sun, 21 Jun 2020 18:51:17: 1000000 INFO @ Sun, 21 Jun 2020 18:51:17: 10000000 INFO @ Sun, 21 Jun 2020 18:51:21: 7000000 INFO @ Sun, 21 Jun 2020 18:51:23: 2000000 INFO @ Sun, 21 Jun 2020 18:51:24: 11000000 INFO @ Sun, 21 Jun 2020 18:51:27: 8000000 INFO @ Sun, 21 Jun 2020 18:51:28: 3000000 INFO @ Sun, 21 Jun 2020 18:51:31: 12000000 INFO @ Sun, 21 Jun 2020 18:51:33: 9000000 INFO @ Sun, 21 Jun 2020 18:51:34: 4000000 INFO @ Sun, 21 Jun 2020 18:51:37: 13000000 INFO @ Sun, 21 Jun 2020 18:51:39: 10000000 INFO @ Sun, 21 Jun 2020 18:51:40: 5000000 INFO @ Sun, 21 Jun 2020 18:51:44: 14000000 INFO @ Sun, 21 Jun 2020 18:51:44: 11000000 INFO @ Sun, 21 Jun 2020 18:51:46: 6000000 INFO @ Sun, 21 Jun 2020 18:51:50: 12000000 INFO @ Sun, 21 Jun 2020 18:51:51: 15000000 INFO @ Sun, 21 Jun 2020 18:51:52: 7000000 INFO @ Sun, 21 Jun 2020 18:51:56: 13000000 INFO @ Sun, 21 Jun 2020 18:51:57: 16000000 INFO @ Sun, 21 Jun 2020 18:51:58: 8000000 INFO @ Sun, 21 Jun 2020 18:52:02: 14000000 INFO @ Sun, 21 Jun 2020 18:52:03: 9000000 INFO @ Sun, 21 Jun 2020 18:52:04: 17000000 INFO @ Sun, 21 Jun 2020 18:52:08: 15000000 INFO @ Sun, 21 Jun 2020 18:52:09: 10000000 INFO @ Sun, 21 Jun 2020 18:52:11: 18000000 INFO @ Sun, 21 Jun 2020 18:52:14: 16000000 INFO @ Sun, 21 Jun 2020 18:52:15: 11000000 INFO @ Sun, 21 Jun 2020 18:52:17: 19000000 INFO @ Sun, 21 Jun 2020 18:52:19: 17000000 INFO @ Sun, 21 Jun 2020 18:52:21: 12000000 INFO @ Sun, 21 Jun 2020 18:52:24: 20000000 INFO @ Sun, 21 Jun 2020 18:52:25: 18000000 INFO @ Sun, 21 Jun 2020 18:52:27: 13000000 INFO @ Sun, 21 Jun 2020 18:52:30: 21000000 INFO @ Sun, 21 Jun 2020 18:52:31: 19000000 INFO @ Sun, 21 Jun 2020 18:52:33: 14000000 INFO @ Sun, 21 Jun 2020 18:52:37: 22000000 INFO @ Sun, 21 Jun 2020 18:52:37: 20000000 INFO @ Sun, 21 Jun 2020 18:52:39: 15000000 INFO @ Sun, 21 Jun 2020 18:52:43: 21000000 INFO @ Sun, 21 Jun 2020 18:52:44: 23000000 INFO @ Sun, 21 Jun 2020 18:52:45: 16000000 INFO @ Sun, 21 Jun 2020 18:52:49: 22000000 INFO @ Sun, 21 Jun 2020 18:52:50: 24000000 INFO @ Sun, 21 Jun 2020 18:52:51: 17000000 INFO @ Sun, 21 Jun 2020 18:52:55: 23000000 INFO @ Sun, 21 Jun 2020 18:52:57: 18000000 INFO @ Sun, 21 Jun 2020 18:52:57: 25000000 INFO @ Sun, 21 Jun 2020 18:53:01: 24000000 INFO @ Sun, 21 Jun 2020 18:53:03: 19000000 INFO @ Sun, 21 Jun 2020 18:53:03: 26000000 INFO @ Sun, 21 Jun 2020 18:53:07: 25000000 INFO @ Sun, 21 Jun 2020 18:53:09: 20000000 INFO @ Sun, 21 Jun 2020 18:53:10: 27000000 INFO @ Sun, 21 Jun 2020 18:53:13: 26000000 INFO @ Sun, 21 Jun 2020 18:53:15: 21000000 INFO @ Sun, 21 Jun 2020 18:53:17: 28000000 INFO @ Sun, 21 Jun 2020 18:53:19: 27000000 INFO @ Sun, 21 Jun 2020 18:53:21: 22000000 INFO @ Sun, 21 Jun 2020 18:53:23: 29000000 INFO @ Sun, 21 Jun 2020 18:53:25: 28000000 INFO @ Sun, 21 Jun 2020 18:53:27: 23000000 INFO @ Sun, 21 Jun 2020 18:53:30: 30000000 INFO @ Sun, 21 Jun 2020 18:53:31: 29000000 INFO @ Sun, 21 Jun 2020 18:53:32: 24000000 INFO @ Sun, 21 Jun 2020 18:53:37: 31000000 INFO @ Sun, 21 Jun 2020 18:53:37: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:53:38: 25000000 INFO @ Sun, 21 Jun 2020 18:53:43: 31000000 INFO @ Sun, 21 Jun 2020 18:53:43: 32000000 INFO @ Sun, 21 Jun 2020 18:53:44: 26000000 INFO @ Sun, 21 Jun 2020 18:53:49: 32000000 INFO @ Sun, 21 Jun 2020 18:53:50: 33000000 INFO @ Sun, 21 Jun 2020 18:53:50: 27000000 INFO @ Sun, 21 Jun 2020 18:53:55: 33000000 INFO @ Sun, 21 Jun 2020 18:53:56: 28000000 INFO @ Sun, 21 Jun 2020 18:53:56: 34000000 INFO @ Sun, 21 Jun 2020 18:54:01: 34000000 INFO @ Sun, 21 Jun 2020 18:54:02: 29000000 INFO @ Sun, 21 Jun 2020 18:54:02: 35000000 INFO @ Sun, 21 Jun 2020 18:54:06: 35000000 INFO @ Sun, 21 Jun 2020 18:54:07: 30000000 INFO @ Sun, 21 Jun 2020 18:54:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:54:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:54:08: #1 total tags in treatment: 35843086 INFO @ Sun, 21 Jun 2020 18:54:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:08: #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 18:54:09: #1 tags after filtering in treatment: 35843025 INFO @ Sun, 21 Jun 2020 18:54:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:12: #2 number of paired peaks: 242 WARNING @ Sun, 21 Jun 2020 18:54:12: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sun, 21 Jun 2020 18:54:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:54:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:54:12: #1 total tags in treatment: 35843086 INFO @ Sun, 21 Jun 2020 18:54:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:12: #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 18:54:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:12: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:54:12: #2 alternative fragment length(s) may be 1,45 bps INFO @ Sun, 21 Jun 2020 18:54:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.05_model.r WARNING @ Sun, 21 Jun 2020 18:54:12: #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 18:54:12: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Sun, 21 Jun 2020 18:54:12: #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 18:54:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:12: #1 tags after filtering in treatment: 35843025 INFO @ Sun, 21 Jun 2020 18:54:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:13: 31000000 INFO @ Sun, 21 Jun 2020 18:54:15: #2 number of paired peaks: 242 WARNING @ Sun, 21 Jun 2020 18:54:15: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sun, 21 Jun 2020 18:54:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:15: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:54:15: #2 alternative fragment length(s) may be 1,45 bps INFO @ Sun, 21 Jun 2020 18:54:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.10_model.r WARNING @ Sun, 21 Jun 2020 18:54:15: #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 18:54:15: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Sun, 21 Jun 2020 18:54:15: #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 18:54:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:19: 32000000 INFO @ Sun, 21 Jun 2020 18:54:24: 33000000 INFO @ Sun, 21 Jun 2020 18:54:29: 34000000 INFO @ Sun, 21 Jun 2020 18:54:34: 35000000 INFO @ Sun, 21 Jun 2020 18:54:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:54:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:54:39: #1 total tags in treatment: 35843086 INFO @ Sun, 21 Jun 2020 18:54:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:39: #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 18:54:40: #1 tags after filtering in treatment: 35843025 INFO @ Sun, 21 Jun 2020 18:54:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:42: #2 number of paired peaks: 242 WARNING @ Sun, 21 Jun 2020 18:54:42: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sun, 21 Jun 2020 18:54:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:42: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:54:42: #2 alternative fragment length(s) may be 1,45 bps INFO @ Sun, 21 Jun 2020 18:54:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.20_model.r WARNING @ Sun, 21 Jun 2020 18:54:42: #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 18:54:42: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Sun, 21 Jun 2020 18:54:42: #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 18:54:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:55:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.05_summits.bed INFO @ Sun, 21 Jun 2020 18:55:28: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:55:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.10_summits.bed INFO @ Sun, 21 Jun 2020 18:55:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:55:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2172426/SRX2172426.20_summits.bed INFO @ Sun, 21 Jun 2020 18:55:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling