Job ID = 6458785 SRX = SRX5436058 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:36:56 prefetch.2.10.7: 1) Downloading 'SRR8637390'... 2020-06-21T12:36:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:40:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:40:21 prefetch.2.10.7: 1) 'SRR8637390' was downloaded successfully Read 41397571 spots for SRR8637390/SRR8637390.sra Written 41397571 spots for SRR8637390/SRR8637390.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: 00:10:10 41397571 reads; of these: 41397571 (100.00%) were unpaired; of these: 2055997 (4.97%) aligned 0 times 28048759 (67.75%) aligned exactly 1 time 11292815 (27.28%) aligned >1 times 95.03% overall alignment rate Time searching: 00:10:10 Overall time: 00:10:10 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] 6965276 / 39341574 = 0.1770 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 22:00:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.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 22:00:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:19: 1000000 INFO @ Sun, 21 Jun 2020 22:00:24: 2000000 INFO @ Sun, 21 Jun 2020 22:00:29: 3000000 INFO @ Sun, 21 Jun 2020 22:00:34: 4000000 INFO @ Sun, 21 Jun 2020 22:00:39: 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 22:00:43: 6000000 INFO @ Sun, 21 Jun 2020 22:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.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 22:00:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:48: 7000000 INFO @ Sun, 21 Jun 2020 22:00:50: 1000000 INFO @ Sun, 21 Jun 2020 22:00:53: 8000000 INFO @ Sun, 21 Jun 2020 22:00:55: 2000000 INFO @ Sun, 21 Jun 2020 22:00:58: 9000000 INFO @ Sun, 21 Jun 2020 22:01:00: 3000000 INFO @ Sun, 21 Jun 2020 22:01:03: 10000000 INFO @ Sun, 21 Jun 2020 22:01:05: 4000000 INFO @ Sun, 21 Jun 2020 22:01:08: 11000000 INFO @ Sun, 21 Jun 2020 22:01:10: 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 22:01:13: 12000000 INFO @ Sun, 21 Jun 2020 22:01:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.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 22:01:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:01:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:01:16: 6000000 INFO @ Sun, 21 Jun 2020 22:01:18: 13000000 INFO @ Sun, 21 Jun 2020 22:01:20: 1000000 INFO @ Sun, 21 Jun 2020 22:01:21: 7000000 INFO @ Sun, 21 Jun 2020 22:01:23: 14000000 INFO @ Sun, 21 Jun 2020 22:01:25: 2000000 INFO @ Sun, 21 Jun 2020 22:01:26: 8000000 INFO @ Sun, 21 Jun 2020 22:01:28: 15000000 INFO @ Sun, 21 Jun 2020 22:01:30: 3000000 INFO @ Sun, 21 Jun 2020 22:01:31: 9000000 INFO @ Sun, 21 Jun 2020 22:01:33: 16000000 INFO @ Sun, 21 Jun 2020 22:01:35: 4000000 INFO @ Sun, 21 Jun 2020 22:01:36: 10000000 INFO @ Sun, 21 Jun 2020 22:01:38: 17000000 INFO @ Sun, 21 Jun 2020 22:01:40: 5000000 INFO @ Sun, 21 Jun 2020 22:01:41: 11000000 INFO @ Sun, 21 Jun 2020 22:01:43: 18000000 INFO @ Sun, 21 Jun 2020 22:01:45: 6000000 INFO @ Sun, 21 Jun 2020 22:01:46: 12000000 INFO @ Sun, 21 Jun 2020 22:01:48: 19000000 INFO @ Sun, 21 Jun 2020 22:01:50: 7000000 INFO @ Sun, 21 Jun 2020 22:01:51: 13000000 INFO @ Sun, 21 Jun 2020 22:01:53: 20000000 INFO @ Sun, 21 Jun 2020 22:01:55: 8000000 INFO @ Sun, 21 Jun 2020 22:01:56: 14000000 INFO @ Sun, 21 Jun 2020 22:01:58: 21000000 INFO @ Sun, 21 Jun 2020 22:02:00: 9000000 INFO @ Sun, 21 Jun 2020 22:02:01: 15000000 INFO @ Sun, 21 Jun 2020 22:02:03: 22000000 INFO @ Sun, 21 Jun 2020 22:02:05: 10000000 INFO @ Sun, 21 Jun 2020 22:02:06: 16000000 INFO @ Sun, 21 Jun 2020 22:02:07: 23000000 INFO @ Sun, 21 Jun 2020 22:02:10: 11000000 INFO @ Sun, 21 Jun 2020 22:02:11: 17000000 INFO @ Sun, 21 Jun 2020 22:02:12: 24000000 INFO @ Sun, 21 Jun 2020 22:02:14: 12000000 INFO @ Sun, 21 Jun 2020 22:02:17: 18000000 INFO @ Sun, 21 Jun 2020 22:02:17: 25000000 INFO @ Sun, 21 Jun 2020 22:02:19: 13000000 INFO @ Sun, 21 Jun 2020 22:02:22: 19000000 INFO @ Sun, 21 Jun 2020 22:02:22: 26000000 INFO @ Sun, 21 Jun 2020 22:02:24: 14000000 INFO @ Sun, 21 Jun 2020 22:02:27: 20000000 INFO @ Sun, 21 Jun 2020 22:02:27: 27000000 INFO @ Sun, 21 Jun 2020 22:02:29: 15000000 INFO @ Sun, 21 Jun 2020 22:02:32: 21000000 INFO @ Sun, 21 Jun 2020 22:02:33: 28000000 INFO @ Sun, 21 Jun 2020 22:02:34: 16000000 INFO @ Sun, 21 Jun 2020 22:02:37: 22000000 INFO @ Sun, 21 Jun 2020 22:02:38: 29000000 INFO @ Sun, 21 Jun 2020 22:02:39: 17000000 INFO @ Sun, 21 Jun 2020 22:02:43: 23000000 INFO @ Sun, 21 Jun 2020 22:02:43: 30000000 INFO @ Sun, 21 Jun 2020 22:02:44: 18000000 INFO @ Sun, 21 Jun 2020 22:02:48: 31000000 INFO @ Sun, 21 Jun 2020 22:02:48: 24000000 INFO @ Sun, 21 Jun 2020 22:02:49: 19000000 INFO @ Sun, 21 Jun 2020 22:02:53: 32000000 INFO @ Sun, 21 Jun 2020 22:02:53: 25000000 INFO @ Sun, 21 Jun 2020 22:02:54: 20000000 INFO @ Sun, 21 Jun 2020 22:02:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:02:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:02:55: #1 total tags in treatment: 32376298 INFO @ Sun, 21 Jun 2020 22:02:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:55: #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 22:02:56: #1 tags after filtering in treatment: 32376253 INFO @ Sun, 21 Jun 2020 22:02:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:58: #2 number of paired peaks: 385 WARNING @ Sun, 21 Jun 2020 22:02:58: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Sun, 21 Jun 2020 22:02:58: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:58: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:58: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:58: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:58: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:02:58: #2 alternative fragment length(s) may be 1,52,593 bps INFO @ Sun, 21 Jun 2020 22:02:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.05_model.r WARNING @ Sun, 21 Jun 2020 22:02:58: #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 22:02:58: #2 You may need to consider one of the other alternative d(s): 1,52,593 WARNING @ Sun, 21 Jun 2020 22:02:58: #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 22:02:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:58: 26000000 INFO @ Sun, 21 Jun 2020 22:02:59: 21000000 INFO @ Sun, 21 Jun 2020 22:03:03: 27000000 INFO @ Sun, 21 Jun 2020 22:03:04: 22000000 INFO @ Sun, 21 Jun 2020 22:03:09: 28000000 INFO @ Sun, 21 Jun 2020 22:03:09: 23000000 INFO @ Sun, 21 Jun 2020 22:03:14: 24000000 INFO @ Sun, 21 Jun 2020 22:03:14: 29000000 INFO @ Sun, 21 Jun 2020 22:03:18: 25000000 INFO @ Sun, 21 Jun 2020 22:03:19: 30000000 INFO @ Sun, 21 Jun 2020 22:03:23: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:03:24: 31000000 INFO @ Sun, 21 Jun 2020 22:03:28: 27000000 INFO @ Sun, 21 Jun 2020 22:03:30: 32000000 INFO @ Sun, 21 Jun 2020 22:03:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:03:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:03:32: #1 total tags in treatment: 32376298 INFO @ Sun, 21 Jun 2020 22:03:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:03:32: #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 22:03:32: #1 tags after filtering in treatment: 32376253 INFO @ Sun, 21 Jun 2020 22:03:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:03:32: #1 finished! INFO @ Sun, 21 Jun 2020 22:03:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:03:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:03:34: 28000000 INFO @ Sun, 21 Jun 2020 22:03:35: #2 number of paired peaks: 385 WARNING @ Sun, 21 Jun 2020 22:03:35: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Sun, 21 Jun 2020 22:03:35: start model_add_line... INFO @ Sun, 21 Jun 2020 22:03:35: start X-correlation... INFO @ Sun, 21 Jun 2020 22:03:35: end of X-cor INFO @ Sun, 21 Jun 2020 22:03:35: #2 finished! INFO @ Sun, 21 Jun 2020 22:03:35: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:03:35: #2 alternative fragment length(s) may be 1,52,593 bps INFO @ Sun, 21 Jun 2020 22:03:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.10_model.r WARNING @ Sun, 21 Jun 2020 22:03:35: #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 22:03:35: #2 You may need to consider one of the other alternative d(s): 1,52,593 WARNING @ Sun, 21 Jun 2020 22:03:35: #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 22:03:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:03:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:03:39: 29000000 INFO @ Sun, 21 Jun 2020 22:03:43: 30000000 INFO @ Sun, 21 Jun 2020 22:03:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:03:48: 31000000 INFO @ Sun, 21 Jun 2020 22:03:53: 32000000 INFO @ Sun, 21 Jun 2020 22:03:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:03:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:03:56: #1 total tags in treatment: 32376298 INFO @ Sun, 21 Jun 2020 22:03:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:03:56: #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 22:03:56: #1 tags after filtering in treatment: 32376253 INFO @ Sun, 21 Jun 2020 22:03:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:03:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:03:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:03:58: #2 number of paired peaks: 385 WARNING @ Sun, 21 Jun 2020 22:03:58: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Sun, 21 Jun 2020 22:03:58: start model_add_line... INFO @ Sun, 21 Jun 2020 22:03:59: start X-correlation... INFO @ Sun, 21 Jun 2020 22:03:59: end of X-cor INFO @ Sun, 21 Jun 2020 22:03:59: #2 finished! INFO @ Sun, 21 Jun 2020 22:03:59: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:03:59: #2 alternative fragment length(s) may be 1,52,593 bps INFO @ Sun, 21 Jun 2020 22:03:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.20_model.r WARNING @ Sun, 21 Jun 2020 22:03:59: #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 22:03:59: #2 You may need to consider one of the other alternative d(s): 1,52,593 WARNING @ Sun, 21 Jun 2020 22:03:59: #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 22:03:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:03:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.05_summits.bed INFO @ Sun, 21 Jun 2020 22:04:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:04:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:04:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.10_summits.bed INFO @ Sun, 21 Jun 2020 22:04:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:04:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436058/SRX5436058.20_summits.bed INFO @ Sun, 21 Jun 2020 22:05:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling