Job ID = 6456740 SRX = SRX3981643 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:02:31 prefetch.2.10.7: 1) Downloading 'SRR7050313'... 2020-06-21T11:02:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:04:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:04:14 prefetch.2.10.7: 'SRR7050313' is valid 2020-06-21T11:04:14 prefetch.2.10.7: 1) 'SRR7050313' was downloaded successfully 2020-06-21T11:04:14 prefetch.2.10.7: 'SRR7050313' has 0 unresolved dependencies Read 14583801 spots for SRR7050313/SRR7050313.sra Written 14583801 spots for SRR7050313/SRR7050313.sra 2020-06-21T11:05:09 prefetch.2.10.7: 1) Downloading 'SRR7050314'... 2020-06-21T11:05:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:07:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:07:04 prefetch.2.10.7: 'SRR7050314' is valid 2020-06-21T11:07:04 prefetch.2.10.7: 1) 'SRR7050314' was downloaded successfully 2020-06-21T11:07:04 prefetch.2.10.7: 'SRR7050314' has 0 unresolved dependencies Read 14472446 spots for SRR7050314/SRR7050314.sra Written 14472446 spots for SRR7050314/SRR7050314.sra 2020-06-21T11:08:03 prefetch.2.10.7: 1) Downloading 'SRR7050315'... 2020-06-21T11:08:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:10:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:10:03 prefetch.2.10.7: 'SRR7050315' is valid 2020-06-21T11:10:03 prefetch.2.10.7: 1) 'SRR7050315' was downloaded successfully 2020-06-21T11:10:03 prefetch.2.10.7: 'SRR7050315' has 0 unresolved dependencies Read 14455423 spots for SRR7050315/SRR7050315.sra Written 14455423 spots for SRR7050315/SRR7050315.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: 00:10:19 43511670 reads; of these: 43511670 (100.00%) were unpaired; of these: 1409017 (3.24%) aligned 0 times 35305775 (81.14%) aligned exactly 1 time 6796878 (15.62%) aligned >1 times 96.76% overall alignment rate Time searching: 00:10:19 Overall time: 00:10:19 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] 9315665 / 42102653 = 0.2213 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 20:30:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.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 20:30:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:42: 1000000 INFO @ Sun, 21 Jun 2020 20:30:47: 2000000 INFO @ Sun, 21 Jun 2020 20:30:52: 3000000 INFO @ Sun, 21 Jun 2020 20:30:57: 4000000 INFO @ Sun, 21 Jun 2020 20:31:02: 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 20:31:06: 6000000 INFO @ Sun, 21 Jun 2020 20:31:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.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 20:31:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:31:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:31:12: 7000000 INFO @ Sun, 21 Jun 2020 20:31:13: 1000000 INFO @ Sun, 21 Jun 2020 20:31:17: 8000000 INFO @ Sun, 21 Jun 2020 20:31:18: 2000000 INFO @ Sun, 21 Jun 2020 20:31:22: 9000000 INFO @ Sun, 21 Jun 2020 20:31:23: 3000000 INFO @ Sun, 21 Jun 2020 20:31:27: 10000000 INFO @ Sun, 21 Jun 2020 20:31:28: 4000000 INFO @ Sun, 21 Jun 2020 20:31:32: 11000000 INFO @ Sun, 21 Jun 2020 20:31:33: 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 20:31:37: 12000000 INFO @ Sun, 21 Jun 2020 20:31:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.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 20:31:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:31:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:31:38: 6000000 INFO @ Sun, 21 Jun 2020 20:31:42: 13000000 INFO @ Sun, 21 Jun 2020 20:31:43: 1000000 INFO @ Sun, 21 Jun 2020 20:31:43: 7000000 INFO @ Sun, 21 Jun 2020 20:31:47: 14000000 INFO @ Sun, 21 Jun 2020 20:31:48: 2000000 INFO @ Sun, 21 Jun 2020 20:31:48: 8000000 INFO @ Sun, 21 Jun 2020 20:31:52: 15000000 INFO @ Sun, 21 Jun 2020 20:31:53: 3000000 INFO @ Sun, 21 Jun 2020 20:31:53: 9000000 INFO @ Sun, 21 Jun 2020 20:31:57: 16000000 INFO @ Sun, 21 Jun 2020 20:31:58: 4000000 INFO @ Sun, 21 Jun 2020 20:31:58: 10000000 INFO @ Sun, 21 Jun 2020 20:32:02: 17000000 INFO @ Sun, 21 Jun 2020 20:32:03: 5000000 INFO @ Sun, 21 Jun 2020 20:32:04: 11000000 INFO @ Sun, 21 Jun 2020 20:32:07: 18000000 INFO @ Sun, 21 Jun 2020 20:32:08: 6000000 INFO @ Sun, 21 Jun 2020 20:32:09: 12000000 INFO @ Sun, 21 Jun 2020 20:32:12: 19000000 INFO @ Sun, 21 Jun 2020 20:32:13: 7000000 INFO @ Sun, 21 Jun 2020 20:32:14: 13000000 INFO @ Sun, 21 Jun 2020 20:32:17: 20000000 INFO @ Sun, 21 Jun 2020 20:32:18: 8000000 INFO @ Sun, 21 Jun 2020 20:32:19: 14000000 INFO @ Sun, 21 Jun 2020 20:32:22: 21000000 INFO @ Sun, 21 Jun 2020 20:32:23: 9000000 INFO @ Sun, 21 Jun 2020 20:32:24: 15000000 INFO @ Sun, 21 Jun 2020 20:32:27: 22000000 INFO @ Sun, 21 Jun 2020 20:32:28: 10000000 INFO @ Sun, 21 Jun 2020 20:32:29: 16000000 INFO @ Sun, 21 Jun 2020 20:32:32: 23000000 INFO @ Sun, 21 Jun 2020 20:32:34: 11000000 INFO @ Sun, 21 Jun 2020 20:32:34: 17000000 INFO @ Sun, 21 Jun 2020 20:32:38: 24000000 INFO @ Sun, 21 Jun 2020 20:32:39: 12000000 INFO @ Sun, 21 Jun 2020 20:32:39: 18000000 INFO @ Sun, 21 Jun 2020 20:32:43: 25000000 INFO @ Sun, 21 Jun 2020 20:32:44: 13000000 INFO @ Sun, 21 Jun 2020 20:32:45: 19000000 INFO @ Sun, 21 Jun 2020 20:32:48: 26000000 INFO @ Sun, 21 Jun 2020 20:32:49: 14000000 INFO @ Sun, 21 Jun 2020 20:32:50: 20000000 INFO @ Sun, 21 Jun 2020 20:32:53: 27000000 INFO @ Sun, 21 Jun 2020 20:32:55: 15000000 INFO @ Sun, 21 Jun 2020 20:32:55: 21000000 INFO @ Sun, 21 Jun 2020 20:32:59: 28000000 INFO @ Sun, 21 Jun 2020 20:33:00: 16000000 INFO @ Sun, 21 Jun 2020 20:33:01: 22000000 INFO @ Sun, 21 Jun 2020 20:33:04: 29000000 INFO @ Sun, 21 Jun 2020 20:33:06: 17000000 INFO @ Sun, 21 Jun 2020 20:33:06: 23000000 INFO @ Sun, 21 Jun 2020 20:33:10: 30000000 INFO @ Sun, 21 Jun 2020 20:33:11: 18000000 INFO @ Sun, 21 Jun 2020 20:33:12: 24000000 INFO @ Sun, 21 Jun 2020 20:33:16: 31000000 INFO @ Sun, 21 Jun 2020 20:33:17: 19000000 INFO @ Sun, 21 Jun 2020 20:33:17: 25000000 INFO @ Sun, 21 Jun 2020 20:33:21: 32000000 INFO @ Sun, 21 Jun 2020 20:33:23: 20000000 INFO @ Sun, 21 Jun 2020 20:33:23: 26000000 INFO @ Sun, 21 Jun 2020 20:33:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:33:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:33:26: #1 total tags in treatment: 32786988 INFO @ Sun, 21 Jun 2020 20:33:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:33:26: #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 20:33:27: #1 tags after filtering in treatment: 32786926 INFO @ Sun, 21 Jun 2020 20:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:33:27: #1 finished! INFO @ Sun, 21 Jun 2020 20:33:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:33:29: 27000000 INFO @ Sun, 21 Jun 2020 20:33:29: 21000000 INFO @ Sun, 21 Jun 2020 20:33:29: #2 number of paired peaks: 609 WARNING @ Sun, 21 Jun 2020 20:33:29: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Sun, 21 Jun 2020 20:33:29: start model_add_line... INFO @ Sun, 21 Jun 2020 20:33:30: start X-correlation... INFO @ Sun, 21 Jun 2020 20:33:30: end of X-cor INFO @ Sun, 21 Jun 2020 20:33:30: #2 finished! INFO @ Sun, 21 Jun 2020 20:33:30: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:33:30: #2 alternative fragment length(s) may be 1,47,69,89,117,163 bps INFO @ Sun, 21 Jun 2020 20:33:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.05_model.r WARNING @ Sun, 21 Jun 2020 20:33:30: #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 20:33:30: #2 You may need to consider one of the other alternative d(s): 1,47,69,89,117,163 WARNING @ Sun, 21 Jun 2020 20:33:30: #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 20:33:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:33:34: 22000000 INFO @ Sun, 21 Jun 2020 20:33:34: 28000000 INFO @ Sun, 21 Jun 2020 20:33:40: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:33:41: 29000000 INFO @ Sun, 21 Jun 2020 20:33:46: 24000000 INFO @ Sun, 21 Jun 2020 20:33:47: 30000000 INFO @ Sun, 21 Jun 2020 20:33:52: 25000000 INFO @ Sun, 21 Jun 2020 20:33:53: 31000000 INFO @ Sun, 21 Jun 2020 20:33:58: 26000000 INFO @ Sun, 21 Jun 2020 20:33:59: 32000000 INFO @ Sun, 21 Jun 2020 20:34:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:34:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:34:04: #1 total tags in treatment: 32786988 INFO @ Sun, 21 Jun 2020 20:34:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:04: #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 20:34:04: 27000000 INFO @ Sun, 21 Jun 2020 20:34:05: #1 tags after filtering in treatment: 32786926 INFO @ Sun, 21 Jun 2020 20:34:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:07: #2 number of paired peaks: 609 WARNING @ Sun, 21 Jun 2020 20:34:07: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Sun, 21 Jun 2020 20:34:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:07: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:07: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:34:07: #2 alternative fragment length(s) may be 1,47,69,89,117,163 bps INFO @ Sun, 21 Jun 2020 20:34:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.10_model.r WARNING @ Sun, 21 Jun 2020 20:34:07: #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 20:34:07: #2 You may need to consider one of the other alternative d(s): 1,47,69,89,117,163 WARNING @ Sun, 21 Jun 2020 20:34:07: #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 20:34:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:10: 28000000 INFO @ Sun, 21 Jun 2020 20:34:16: 29000000 INFO @ Sun, 21 Jun 2020 20:34:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:21: 30000000 INFO @ Sun, 21 Jun 2020 20:34:27: 31000000 INFO @ Sun, 21 Jun 2020 20:34:33: 32000000 INFO @ Sun, 21 Jun 2020 20:34:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:34:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:34:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.05_summits.bed INFO @ Sun, 21 Jun 2020 20:34:37: Done! INFO @ Sun, 21 Jun 2020 20:34:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:34:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:34:38: #1 total tags in treatment: 32786988 INFO @ Sun, 21 Jun 2020 20:34:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:34:39: #1 tags after filtering in treatment: 32786926 INFO @ Sun, 21 Jun 2020 20:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:41: #2 number of paired peaks: 609 WARNING @ Sun, 21 Jun 2020 20:34:41: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Sun, 21 Jun 2020 20:34:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:41: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:34:41: #2 alternative fragment length(s) may be 1,47,69,89,117,163 bps INFO @ Sun, 21 Jun 2020 20:34:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.20_model.r WARNING @ Sun, 21 Jun 2020 20:34:41: #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 20:34:41: #2 You may need to consider one of the other alternative d(s): 1,47,69,89,117,163 WARNING @ Sun, 21 Jun 2020 20:34:41: #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 20:34:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:35:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:35:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:35:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.10_summits.bed INFO @ Sun, 21 Jun 2020 20:35:17: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:35:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:35:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:35:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:35:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981643/SRX3981643.20_summits.bed INFO @ Sun, 21 Jun 2020 20:35:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling