Job ID = 6456725 SRX = SRX3981629 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:10:54 prefetch.2.10.7: 1) Downloading 'SRR7050271'... 2020-06-21T11:10:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:13:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:13:10 prefetch.2.10.7: 'SRR7050271' is valid 2020-06-21T11:13:10 prefetch.2.10.7: 1) 'SRR7050271' was downloaded successfully 2020-06-21T11:13:10 prefetch.2.10.7: 'SRR7050271' has 0 unresolved dependencies Read 12901046 spots for SRR7050271/SRR7050271.sra Written 12901046 spots for SRR7050271/SRR7050271.sra 2020-06-21T11:14:02 prefetch.2.10.7: 1) Downloading 'SRR7050272'... 2020-06-21T11:14:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:15:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:15:44 prefetch.2.10.7: 'SRR7050272' is valid 2020-06-21T11:15:44 prefetch.2.10.7: 1) 'SRR7050272' was downloaded successfully 2020-06-21T11:15:44 prefetch.2.10.7: 'SRR7050272' has 0 unresolved dependencies Read 12801479 spots for SRR7050272/SRR7050272.sra Written 12801479 spots for SRR7050272/SRR7050272.sra 2020-06-21T11:16:40 prefetch.2.10.7: 1) Downloading 'SRR7050273'... 2020-06-21T11:16:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:17:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:17:41 prefetch.2.10.7: 'SRR7050273' is valid 2020-06-21T11:17:41 prefetch.2.10.7: 1) 'SRR7050273' was downloaded successfully 2020-06-21T11:17:41 prefetch.2.10.7: 'SRR7050273' has 0 unresolved dependencies Read 12770531 spots for SRR7050273/SRR7050273.sra Written 12770531 spots for SRR7050273/SRR7050273.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: 00:10:14 38473056 reads; of these: 38473056 (100.00%) were unpaired; of these: 1412685 (3.67%) aligned 0 times 28269051 (73.48%) aligned exactly 1 time 8791320 (22.85%) aligned >1 times 96.33% overall alignment rate Time searching: 00:10:14 Overall time: 00:10:14 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] 4722535 / 37060371 = 0.1274 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 20:38:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.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 20:38:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:38:29: 1000000 INFO @ Sun, 21 Jun 2020 20:38:34: 2000000 INFO @ Sun, 21 Jun 2020 20:38:39: 3000000 INFO @ Sun, 21 Jun 2020 20:38:44: 4000000 INFO @ Sun, 21 Jun 2020 20:38:49: 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 20:38:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.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 20:38:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:38:54: 6000000 INFO @ Sun, 21 Jun 2020 20:38:59: 1000000 INFO @ Sun, 21 Jun 2020 20:39:00: 7000000 INFO @ Sun, 21 Jun 2020 20:39:05: 2000000 INFO @ Sun, 21 Jun 2020 20:39:05: 8000000 INFO @ Sun, 21 Jun 2020 20:39:10: 3000000 INFO @ Sun, 21 Jun 2020 20:39:10: 9000000 INFO @ Sun, 21 Jun 2020 20:39:15: 4000000 INFO @ Sun, 21 Jun 2020 20:39:16: 10000000 INFO @ Sun, 21 Jun 2020 20:39:21: 5000000 INFO @ Sun, 21 Jun 2020 20:39:21: 11000000 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 20:39:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.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 20:39:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:26: 6000000 INFO @ Sun, 21 Jun 2020 20:39:26: 12000000 INFO @ Sun, 21 Jun 2020 20:39:30: 1000000 INFO @ Sun, 21 Jun 2020 20:39:32: 7000000 INFO @ Sun, 21 Jun 2020 20:39:32: 13000000 INFO @ Sun, 21 Jun 2020 20:39:35: 2000000 INFO @ Sun, 21 Jun 2020 20:39:37: 8000000 INFO @ Sun, 21 Jun 2020 20:39:37: 14000000 INFO @ Sun, 21 Jun 2020 20:39:41: 3000000 INFO @ Sun, 21 Jun 2020 20:39:43: 15000000 INFO @ Sun, 21 Jun 2020 20:39:43: 9000000 INFO @ Sun, 21 Jun 2020 20:39:47: 4000000 INFO @ Sun, 21 Jun 2020 20:39:48: 16000000 INFO @ Sun, 21 Jun 2020 20:39:48: 10000000 INFO @ Sun, 21 Jun 2020 20:39:53: 5000000 INFO @ Sun, 21 Jun 2020 20:39:53: 17000000 INFO @ Sun, 21 Jun 2020 20:39:54: 11000000 INFO @ Sun, 21 Jun 2020 20:39:59: 6000000 INFO @ Sun, 21 Jun 2020 20:39:59: 18000000 INFO @ Sun, 21 Jun 2020 20:39:59: 12000000 INFO @ Sun, 21 Jun 2020 20:40:04: 19000000 INFO @ Sun, 21 Jun 2020 20:40:05: 7000000 INFO @ Sun, 21 Jun 2020 20:40:05: 13000000 INFO @ Sun, 21 Jun 2020 20:40:10: 20000000 INFO @ Sun, 21 Jun 2020 20:40:10: 14000000 INFO @ Sun, 21 Jun 2020 20:40:11: 8000000 INFO @ Sun, 21 Jun 2020 20:40:15: 21000000 INFO @ Sun, 21 Jun 2020 20:40:16: 15000000 INFO @ Sun, 21 Jun 2020 20:40:17: 9000000 INFO @ Sun, 21 Jun 2020 20:40:21: 22000000 INFO @ Sun, 21 Jun 2020 20:40:21: 16000000 INFO @ Sun, 21 Jun 2020 20:40:23: 10000000 INFO @ Sun, 21 Jun 2020 20:40:26: 23000000 INFO @ Sun, 21 Jun 2020 20:40:27: 17000000 INFO @ Sun, 21 Jun 2020 20:40:29: 11000000 INFO @ Sun, 21 Jun 2020 20:40:32: 24000000 INFO @ Sun, 21 Jun 2020 20:40:33: 18000000 INFO @ Sun, 21 Jun 2020 20:40:34: 12000000 INFO @ Sun, 21 Jun 2020 20:40:38: 25000000 INFO @ Sun, 21 Jun 2020 20:40:38: 19000000 INFO @ Sun, 21 Jun 2020 20:40:40: 13000000 INFO @ Sun, 21 Jun 2020 20:40:43: 26000000 INFO @ Sun, 21 Jun 2020 20:40:44: 20000000 INFO @ Sun, 21 Jun 2020 20:40:46: 14000000 INFO @ Sun, 21 Jun 2020 20:40:49: 27000000 INFO @ Sun, 21 Jun 2020 20:40:49: 21000000 INFO @ Sun, 21 Jun 2020 20:40:52: 15000000 INFO @ Sun, 21 Jun 2020 20:40:55: 22000000 INFO @ Sun, 21 Jun 2020 20:40:55: 28000000 INFO @ Sun, 21 Jun 2020 20:40:58: 16000000 INFO @ Sun, 21 Jun 2020 20:41:01: 23000000 INFO @ Sun, 21 Jun 2020 20:41:01: 29000000 INFO @ Sun, 21 Jun 2020 20:41:04: 17000000 INFO @ Sun, 21 Jun 2020 20:41:07: 24000000 INFO @ Sun, 21 Jun 2020 20:41:07: 30000000 INFO @ Sun, 21 Jun 2020 20:41:10: 18000000 INFO @ Sun, 21 Jun 2020 20:41:13: 31000000 INFO @ Sun, 21 Jun 2020 20:41:13: 25000000 INFO @ Sun, 21 Jun 2020 20:41:17: 19000000 INFO @ Sun, 21 Jun 2020 20:41:18: 32000000 INFO @ Sun, 21 Jun 2020 20:41:19: 26000000 INFO @ Sun, 21 Jun 2020 20:41:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:41:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:41:21: #1 total tags in treatment: 32337836 INFO @ Sun, 21 Jun 2020 20:41:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:21: #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 20:41:22: #1 tags after filtering in treatment: 32337799 INFO @ Sun, 21 Jun 2020 20:41:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:22: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:23: 20000000 INFO @ Sun, 21 Jun 2020 20:41:24: #2 number of paired peaks: 180 WARNING @ Sun, 21 Jun 2020 20:41:24: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sun, 21 Jun 2020 20:41:24: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:24: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:24: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:24: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:24: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:41:24: #2 alternative fragment length(s) may be 2,56,567 bps INFO @ Sun, 21 Jun 2020 20:41:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.05_model.r WARNING @ Sun, 21 Jun 2020 20:41:24: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:41:24: #2 You may need to consider one of the other alternative d(s): 2,56,567 WARNING @ Sun, 21 Jun 2020 20:41:24: #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 20:41:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:24: 27000000 INFO @ Sun, 21 Jun 2020 20:41:29: 21000000 INFO @ Sun, 21 Jun 2020 20:41:31: 28000000 INFO @ Sun, 21 Jun 2020 20:41:35: 22000000 INFO @ Sun, 21 Jun 2020 20:41:37: 29000000 INFO @ Sun, 21 Jun 2020 20:41:41: 23000000 INFO @ Sun, 21 Jun 2020 20:41:42: 30000000 INFO @ Sun, 21 Jun 2020 20:41:47: 24000000 INFO @ Sun, 21 Jun 2020 20:41:48: 31000000 INFO @ Sun, 21 Jun 2020 20:41:53: 25000000 INFO @ Sun, 21 Jun 2020 20:41:54: 32000000 INFO @ Sun, 21 Jun 2020 20:41:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:41:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:41:56: #1 total tags in treatment: 32337836 INFO @ Sun, 21 Jun 2020 20:41:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:56: #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 20:41:57: #1 tags after filtering in treatment: 32337799 INFO @ Sun, 21 Jun 2020 20:41:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:57: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:59: #2 number of paired peaks: 180 WARNING @ Sun, 21 Jun 2020 20:41:59: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sun, 21 Jun 2020 20:41:59: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:59: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:59: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:59: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:59: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:41:59: #2 alternative fragment length(s) may be 2,56,567 bps INFO @ Sun, 21 Jun 2020 20:41:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.10_model.r WARNING @ Sun, 21 Jun 2020 20:41:59: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:41:59: #2 You may need to consider one of the other alternative d(s): 2,56,567 WARNING @ Sun, 21 Jun 2020 20:41:59: #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 20:41:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:42:00: 26000000 INFO @ Sun, 21 Jun 2020 20:42:06: 27000000 INFO @ Sun, 21 Jun 2020 20:42:12: 28000000 INFO @ Sun, 21 Jun 2020 20:42:18: 29000000 INFO @ Sun, 21 Jun 2020 20:42:19: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:42:24: 30000000 INFO @ Sun, 21 Jun 2020 20:42:29: 31000000 INFO @ Sun, 21 Jun 2020 20:42:35: 32000000 INFO @ Sun, 21 Jun 2020 20:42:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:42:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:42:38: #1 total tags in treatment: 32337836 INFO @ Sun, 21 Jun 2020 20:42:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:38: #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 20:42:39: #1 tags after filtering in treatment: 32337799 INFO @ Sun, 21 Jun 2020 20:42:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:41: #2 number of paired peaks: 180 WARNING @ Sun, 21 Jun 2020 20:42:41: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sun, 21 Jun 2020 20:42:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:41: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:42:41: #2 alternative fragment length(s) may be 2,56,567 bps INFO @ Sun, 21 Jun 2020 20:42:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.20_model.r WARNING @ Sun, 21 Jun 2020 20:42:41: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:42:41: #2 You may need to consider one of the other alternative d(s): 2,56,567 WARNING @ Sun, 21 Jun 2020 20:42:41: #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 20:42:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:42:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:42:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:42:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.05_summits.bed INFO @ Sun, 21 Jun 2020 20:42:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:42:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.10_summits.bed INFO @ Sun, 21 Jun 2020 20:43:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:43:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:43:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981629/SRX3981629.20_summits.bed INFO @ Sun, 21 Jun 2020 20:43:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling