Job ID = 6456835 SRX = SRX3981722 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:24:24 prefetch.2.10.7: 1) Downloading 'SRR7050578'... 2020-06-21T11:24:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:25:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:25:59 prefetch.2.10.7: 'SRR7050578' is valid 2020-06-21T11:25:59 prefetch.2.10.7: 1) 'SRR7050578' was downloaded successfully 2020-06-21T11:25:59 prefetch.2.10.7: 'SRR7050578' has 0 unresolved dependencies Read 13346840 spots for SRR7050578/SRR7050578.sra Written 13346840 spots for SRR7050578/SRR7050578.sra 2020-06-21T11:26:53 prefetch.2.10.7: 1) Downloading 'SRR7050579'... 2020-06-21T11:26:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:27:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:27:41 prefetch.2.10.7: 'SRR7050579' is valid 2020-06-21T11:27:41 prefetch.2.10.7: 1) 'SRR7050579' was downloaded successfully 2020-06-21T11:27:41 prefetch.2.10.7: 'SRR7050579' has 0 unresolved dependencies Read 13499766 spots for SRR7050579/SRR7050579.sra Written 13499766 spots for SRR7050579/SRR7050579.sra 2020-06-21T11:28:33 prefetch.2.10.7: 1) Downloading 'SRR7050580'... 2020-06-21T11:28:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:29:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:29:53 prefetch.2.10.7: 'SRR7050580' is valid 2020-06-21T11:29:53 prefetch.2.10.7: 1) 'SRR7050580' was downloaded successfully 2020-06-21T11:29:53 prefetch.2.10.7: 'SRR7050580' has 0 unresolved dependencies Read 13550595 spots for SRR7050580/SRR7050580.sra Written 13550595 spots for SRR7050580/SRR7050580.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: 00:10:33 40397201 reads; of these: 40397201 (100.00%) were unpaired; of these: 1203247 (2.98%) aligned 0 times 28365646 (70.22%) aligned exactly 1 time 10828308 (26.80%) aligned >1 times 97.02% overall alignment rate Time searching: 00:10:33 Overall time: 00:10:33 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] 5567648 / 39193954 = 0.1421 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 20:49:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.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 20:49:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:49:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:49:27: 1000000 INFO @ Sun, 21 Jun 2020 20:49:32: 2000000 INFO @ Sun, 21 Jun 2020 20:49:37: 3000000 INFO @ Sun, 21 Jun 2020 20:49:42: 4000000 INFO @ Sun, 21 Jun 2020 20:49:47: 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 20:49:52: 6000000 INFO @ Sun, 21 Jun 2020 20:49:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.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 20:49:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:49:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:49:57: 7000000 INFO @ Sun, 21 Jun 2020 20:49:57: 1000000 INFO @ Sun, 21 Jun 2020 20:50:02: 8000000 INFO @ Sun, 21 Jun 2020 20:50:03: 2000000 INFO @ Sun, 21 Jun 2020 20:50:07: 9000000 INFO @ Sun, 21 Jun 2020 20:50:08: 3000000 INFO @ Sun, 21 Jun 2020 20:50:12: 10000000 INFO @ Sun, 21 Jun 2020 20:50:13: 4000000 INFO @ Sun, 21 Jun 2020 20:50:17: 11000000 INFO @ Sun, 21 Jun 2020 20:50:18: 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 20:50:22: 12000000 INFO @ Sun, 21 Jun 2020 20:50:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.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 20:50:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:50:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:50:24: 6000000 INFO @ Sun, 21 Jun 2020 20:50:27: 13000000 INFO @ Sun, 21 Jun 2020 20:50:27: 1000000 INFO @ Sun, 21 Jun 2020 20:50:29: 7000000 INFO @ Sun, 21 Jun 2020 20:50:33: 14000000 INFO @ Sun, 21 Jun 2020 20:50:33: 2000000 INFO @ Sun, 21 Jun 2020 20:50:34: 8000000 INFO @ Sun, 21 Jun 2020 20:50:38: 15000000 INFO @ Sun, 21 Jun 2020 20:50:38: 3000000 INFO @ Sun, 21 Jun 2020 20:50:39: 9000000 INFO @ Sun, 21 Jun 2020 20:50:43: 16000000 INFO @ Sun, 21 Jun 2020 20:50:43: 4000000 INFO @ Sun, 21 Jun 2020 20:50:45: 10000000 INFO @ Sun, 21 Jun 2020 20:50:48: 17000000 INFO @ Sun, 21 Jun 2020 20:50:49: 5000000 INFO @ Sun, 21 Jun 2020 20:50:50: 11000000 INFO @ Sun, 21 Jun 2020 20:50:53: 18000000 INFO @ Sun, 21 Jun 2020 20:50:54: 6000000 INFO @ Sun, 21 Jun 2020 20:50:55: 12000000 INFO @ Sun, 21 Jun 2020 20:50:59: 19000000 INFO @ Sun, 21 Jun 2020 20:50:59: 7000000 INFO @ Sun, 21 Jun 2020 20:51:00: 13000000 INFO @ Sun, 21 Jun 2020 20:51:04: 20000000 INFO @ Sun, 21 Jun 2020 20:51:04: 8000000 INFO @ Sun, 21 Jun 2020 20:51:06: 14000000 INFO @ Sun, 21 Jun 2020 20:51:09: 21000000 INFO @ Sun, 21 Jun 2020 20:51:09: 9000000 INFO @ Sun, 21 Jun 2020 20:51:11: 15000000 INFO @ Sun, 21 Jun 2020 20:51:14: 22000000 INFO @ Sun, 21 Jun 2020 20:51:14: 10000000 INFO @ Sun, 21 Jun 2020 20:51:16: 16000000 INFO @ Sun, 21 Jun 2020 20:51:19: 23000000 INFO @ Sun, 21 Jun 2020 20:51:20: 11000000 INFO @ Sun, 21 Jun 2020 20:51:21: 17000000 INFO @ Sun, 21 Jun 2020 20:51:24: 24000000 INFO @ Sun, 21 Jun 2020 20:51:25: 12000000 INFO @ Sun, 21 Jun 2020 20:51:26: 18000000 INFO @ Sun, 21 Jun 2020 20:51:30: 25000000 INFO @ Sun, 21 Jun 2020 20:51:30: 13000000 INFO @ Sun, 21 Jun 2020 20:51:32: 19000000 INFO @ Sun, 21 Jun 2020 20:51:35: 26000000 INFO @ Sun, 21 Jun 2020 20:51:35: 14000000 INFO @ Sun, 21 Jun 2020 20:51:37: 20000000 INFO @ Sun, 21 Jun 2020 20:51:40: 27000000 INFO @ Sun, 21 Jun 2020 20:51:40: 15000000 INFO @ Sun, 21 Jun 2020 20:51:42: 21000000 INFO @ Sun, 21 Jun 2020 20:51:45: 28000000 INFO @ Sun, 21 Jun 2020 20:51:46: 16000000 INFO @ Sun, 21 Jun 2020 20:51:47: 22000000 INFO @ Sun, 21 Jun 2020 20:51:51: 17000000 INFO @ Sun, 21 Jun 2020 20:51:51: 29000000 INFO @ Sun, 21 Jun 2020 20:51:52: 23000000 INFO @ Sun, 21 Jun 2020 20:51:56: 18000000 INFO @ Sun, 21 Jun 2020 20:51:56: 30000000 INFO @ Sun, 21 Jun 2020 20:51:58: 24000000 INFO @ Sun, 21 Jun 2020 20:52:01: 19000000 INFO @ Sun, 21 Jun 2020 20:52:02: 31000000 INFO @ Sun, 21 Jun 2020 20:52:03: 25000000 INFO @ Sun, 21 Jun 2020 20:52:06: 20000000 INFO @ Sun, 21 Jun 2020 20:52:07: 32000000 INFO @ Sun, 21 Jun 2020 20:52:08: 26000000 INFO @ Sun, 21 Jun 2020 20:52:12: 21000000 INFO @ Sun, 21 Jun 2020 20:52:13: 33000000 INFO @ Sun, 21 Jun 2020 20:52:14: 27000000 INFO @ Sun, 21 Jun 2020 20:52:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:52:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:52:17: #1 total tags in treatment: 33626306 INFO @ Sun, 21 Jun 2020 20:52:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:17: #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 20:52:17: 22000000 INFO @ Sun, 21 Jun 2020 20:52:17: #1 tags after filtering in treatment: 33626264 INFO @ Sun, 21 Jun 2020 20:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:19: 28000000 INFO @ Sun, 21 Jun 2020 20:52:20: #2 number of paired peaks: 218 WARNING @ Sun, 21 Jun 2020 20:52:20: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Sun, 21 Jun 2020 20:52:20: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:20: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:20: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:20: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:20: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:52:20: #2 alternative fragment length(s) may be 1,10,45,558,578 bps INFO @ Sun, 21 Jun 2020 20:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.05_model.r WARNING @ Sun, 21 Jun 2020 20:52:20: #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 20:52:20: #2 You may need to consider one of the other alternative d(s): 1,10,45,558,578 WARNING @ Sun, 21 Jun 2020 20:52:20: #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 20:52:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:52:22: 23000000 INFO @ Sun, 21 Jun 2020 20:52:25: 29000000 INFO @ Sun, 21 Jun 2020 20:52:27: 24000000 INFO @ Sun, 21 Jun 2020 20:52:30: 30000000 INFO @ Sun, 21 Jun 2020 20:52:33: 25000000 INFO @ Sun, 21 Jun 2020 20:52:35: 31000000 INFO @ Sun, 21 Jun 2020 20:52:38: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:52:40: 32000000 INFO @ Sun, 21 Jun 2020 20:52:43: 27000000 INFO @ Sun, 21 Jun 2020 20:52:46: 33000000 INFO @ Sun, 21 Jun 2020 20:52:48: 28000000 INFO @ Sun, 21 Jun 2020 20:52:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:52:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:52:50: #1 total tags in treatment: 33626306 INFO @ Sun, 21 Jun 2020 20:52:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:50: #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 20:52:50: #1 tags after filtering in treatment: 33626264 INFO @ Sun, 21 Jun 2020 20:52:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:50: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:53: #2 number of paired peaks: 218 WARNING @ Sun, 21 Jun 2020 20:52:53: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Sun, 21 Jun 2020 20:52:53: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:53: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:53: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:53: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:53: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:52:53: #2 alternative fragment length(s) may be 1,10,45,558,578 bps INFO @ Sun, 21 Jun 2020 20:52:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.10_model.r WARNING @ Sun, 21 Jun 2020 20:52:53: #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 20:52:53: #2 You may need to consider one of the other alternative d(s): 1,10,45,558,578 WARNING @ Sun, 21 Jun 2020 20:52:53: #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 20:52:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:52:54: 29000000 INFO @ Sun, 21 Jun 2020 20:52:59: 30000000 INFO @ Sun, 21 Jun 2020 20:53:04: 31000000 INFO @ Sun, 21 Jun 2020 20:53:09: 32000000 INFO @ Sun, 21 Jun 2020 20:53:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:53:14: 33000000 INFO @ Sun, 21 Jun 2020 20:53:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:53:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:53:17: #1 total tags in treatment: 33626306 INFO @ Sun, 21 Jun 2020 20:53:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:53:17: #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 20:53:18: #1 tags after filtering in treatment: 33626264 INFO @ Sun, 21 Jun 2020 20:53:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:53:18: #1 finished! INFO @ Sun, 21 Jun 2020 20:53:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:53:20: #2 number of paired peaks: 218 WARNING @ Sun, 21 Jun 2020 20:53:20: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Sun, 21 Jun 2020 20:53:20: start model_add_line... INFO @ Sun, 21 Jun 2020 20:53:20: start X-correlation... INFO @ Sun, 21 Jun 2020 20:53:20: end of X-cor INFO @ Sun, 21 Jun 2020 20:53:20: #2 finished! INFO @ Sun, 21 Jun 2020 20:53:20: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:53:20: #2 alternative fragment length(s) may be 1,10,45,558,578 bps INFO @ Sun, 21 Jun 2020 20:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.20_model.r WARNING @ Sun, 21 Jun 2020 20:53:20: #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 20:53:20: #2 You may need to consider one of the other alternative d(s): 1,10,45,558,578 WARNING @ Sun, 21 Jun 2020 20:53:20: #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 20:53:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:53:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:53:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:53:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.05_summits.bed INFO @ Sun, 21 Jun 2020 20:53:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:53:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:54:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:54:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:54:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.10_summits.bed INFO @ Sun, 21 Jun 2020 20:54:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:54:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:54:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:54:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:54:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981722/SRX3981722.20_summits.bed INFO @ Sun, 21 Jun 2020 20:54:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling