Job ID = 6458584 SRX = SRX5343120 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:31:37 prefetch.2.10.7: 1) Downloading 'SRR8540820'... 2020-06-21T12:31:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:37:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:37:17 prefetch.2.10.7: 1) 'SRR8540820' was downloaded successfully 2020-06-21T12:37:17 prefetch.2.10.7: 'SRR8540820' has 0 unresolved dependencies Read 34725899 spots for SRR8540820/SRR8540820.sra Written 34725899 spots for SRR8540820/SRR8540820.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: 00:12:59 34725899 reads; of these: 34725899 (100.00%) were unpaired; of these: 1558689 (4.49%) aligned 0 times 23117436 (66.57%) aligned exactly 1 time 10049774 (28.94%) aligned >1 times 95.51% overall alignment rate Time searching: 00:12:59 Overall time: 00:12:59 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] 5368255 / 33167210 = 0.1619 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 22:02:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.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 22:02:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:02:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:02:29: 1000000 INFO @ Sun, 21 Jun 2020 22:02:36: 2000000 INFO @ Sun, 21 Jun 2020 22:02:43: 3000000 INFO @ Sun, 21 Jun 2020 22:02:50: 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 22:02:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.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 22:02:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:02:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:02:57: 5000000 INFO @ Sun, 21 Jun 2020 22:03:00: 1000000 INFO @ Sun, 21 Jun 2020 22:03:04: 6000000 INFO @ Sun, 21 Jun 2020 22:03:06: 2000000 INFO @ Sun, 21 Jun 2020 22:03:11: 7000000 INFO @ Sun, 21 Jun 2020 22:03:13: 3000000 INFO @ Sun, 21 Jun 2020 22:03:19: 8000000 INFO @ Sun, 21 Jun 2020 22:03:20: 4000000 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 22:03:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.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 22:03:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:26: 9000000 INFO @ Sun, 21 Jun 2020 22:03:27: 5000000 INFO @ Sun, 21 Jun 2020 22:03:30: 1000000 INFO @ Sun, 21 Jun 2020 22:03:33: 10000000 INFO @ Sun, 21 Jun 2020 22:03:34: 6000000 INFO @ Sun, 21 Jun 2020 22:03:37: 2000000 INFO @ Sun, 21 Jun 2020 22:03:40: 7000000 INFO @ Sun, 21 Jun 2020 22:03:41: 11000000 INFO @ Sun, 21 Jun 2020 22:03:44: 3000000 INFO @ Sun, 21 Jun 2020 22:03:47: 8000000 INFO @ Sun, 21 Jun 2020 22:03:48: 12000000 INFO @ Sun, 21 Jun 2020 22:03:51: 4000000 INFO @ Sun, 21 Jun 2020 22:03:54: 9000000 INFO @ Sun, 21 Jun 2020 22:03:55: 13000000 INFO @ Sun, 21 Jun 2020 22:03:57: 5000000 INFO @ Sun, 21 Jun 2020 22:04:01: 10000000 INFO @ Sun, 21 Jun 2020 22:04:02: 14000000 INFO @ Sun, 21 Jun 2020 22:04:04: 6000000 INFO @ Sun, 21 Jun 2020 22:04:08: 11000000 INFO @ Sun, 21 Jun 2020 22:04:10: 15000000 INFO @ Sun, 21 Jun 2020 22:04:11: 7000000 INFO @ Sun, 21 Jun 2020 22:04:15: 12000000 INFO @ Sun, 21 Jun 2020 22:04:17: 16000000 INFO @ Sun, 21 Jun 2020 22:04:18: 8000000 INFO @ Sun, 21 Jun 2020 22:04:22: 13000000 INFO @ Sun, 21 Jun 2020 22:04:24: 17000000 INFO @ Sun, 21 Jun 2020 22:04:25: 9000000 INFO @ Sun, 21 Jun 2020 22:04:29: 14000000 INFO @ Sun, 21 Jun 2020 22:04:32: 18000000 INFO @ Sun, 21 Jun 2020 22:04:33: 10000000 INFO @ Sun, 21 Jun 2020 22:04:36: 15000000 INFO @ Sun, 21 Jun 2020 22:04:39: 19000000 INFO @ Sun, 21 Jun 2020 22:04:40: 11000000 INFO @ Sun, 21 Jun 2020 22:04:43: 16000000 INFO @ Sun, 21 Jun 2020 22:04:46: 20000000 INFO @ Sun, 21 Jun 2020 22:04:47: 12000000 INFO @ Sun, 21 Jun 2020 22:04:50: 17000000 INFO @ Sun, 21 Jun 2020 22:04:54: 21000000 INFO @ Sun, 21 Jun 2020 22:04:54: 13000000 INFO @ Sun, 21 Jun 2020 22:04:57: 18000000 INFO @ Sun, 21 Jun 2020 22:05:01: 14000000 INFO @ Sun, 21 Jun 2020 22:05:01: 22000000 INFO @ Sun, 21 Jun 2020 22:05:04: 19000000 INFO @ Sun, 21 Jun 2020 22:05:08: 15000000 INFO @ Sun, 21 Jun 2020 22:05:08: 23000000 INFO @ Sun, 21 Jun 2020 22:05:11: 20000000 INFO @ Sun, 21 Jun 2020 22:05:15: 16000000 INFO @ Sun, 21 Jun 2020 22:05:16: 24000000 INFO @ Sun, 21 Jun 2020 22:05:18: 21000000 INFO @ Sun, 21 Jun 2020 22:05:22: 17000000 INFO @ Sun, 21 Jun 2020 22:05:24: 25000000 INFO @ Sun, 21 Jun 2020 22:05:25: 22000000 INFO @ Sun, 21 Jun 2020 22:05:29: 18000000 INFO @ Sun, 21 Jun 2020 22:05:31: 26000000 INFO @ Sun, 21 Jun 2020 22:05:32: 23000000 INFO @ Sun, 21 Jun 2020 22:05:36: 19000000 INFO @ Sun, 21 Jun 2020 22:05:39: 27000000 INFO @ Sun, 21 Jun 2020 22:05:40: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:05:43: 20000000 INFO @ Sun, 21 Jun 2020 22:05:45: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:05:45: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:05:45: #1 total tags in treatment: 27798955 INFO @ Sun, 21 Jun 2020 22:05:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:45: #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 22:05:46: #1 tags after filtering in treatment: 27798954 INFO @ Sun, 21 Jun 2020 22:05:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:46: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:47: 25000000 INFO @ Sun, 21 Jun 2020 22:05:48: #2 number of paired peaks: 185 WARNING @ Sun, 21 Jun 2020 22:05:48: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:48: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:48: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:48: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:48: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:48: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:05:48: #2 alternative fragment length(s) may be 2,35 bps INFO @ Sun, 21 Jun 2020 22:05:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.05_model.r WARNING @ Sun, 21 Jun 2020 22:05:48: #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 22:05:48: #2 You may need to consider one of the other alternative d(s): 2,35 WARNING @ Sun, 21 Jun 2020 22:05:48: #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 22:05:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:50: 21000000 INFO @ Sun, 21 Jun 2020 22:05:54: 26000000 INFO @ Sun, 21 Jun 2020 22:05:57: 22000000 INFO @ Sun, 21 Jun 2020 22:06:01: 27000000 INFO @ Sun, 21 Jun 2020 22:06:04: 23000000 INFO @ Sun, 21 Jun 2020 22:06:06: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:06:06: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:06:06: #1 total tags in treatment: 27798955 INFO @ Sun, 21 Jun 2020 22:06:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:06: #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 22:06:07: #1 tags after filtering in treatment: 27798954 INFO @ Sun, 21 Jun 2020 22:06:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:07: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:09: #2 number of paired peaks: 185 WARNING @ Sun, 21 Jun 2020 22:06:09: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sun, 21 Jun 2020 22:06:09: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:09: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:09: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:09: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:09: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:06:09: #2 alternative fragment length(s) may be 2,35 bps INFO @ Sun, 21 Jun 2020 22:06:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.10_model.r WARNING @ Sun, 21 Jun 2020 22:06:09: #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 22:06:09: #2 You may need to consider one of the other alternative d(s): 2,35 WARNING @ Sun, 21 Jun 2020 22:06:09: #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 22:06:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:06:10: 24000000 INFO @ Sun, 21 Jun 2020 22:06:17: 25000000 INFO @ Sun, 21 Jun 2020 22:06:23: 26000000 INFO @ Sun, 21 Jun 2020 22:06:30: 27000000 INFO @ Sun, 21 Jun 2020 22:06:35: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:06:35: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:06:35: #1 total tags in treatment: 27798955 INFO @ Sun, 21 Jun 2020 22:06:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:35: #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 22:06:36: #1 tags after filtering in treatment: 27798954 INFO @ Sun, 21 Jun 2020 22:06:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:36: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:06:37: #2 number of paired peaks: 185 WARNING @ Sun, 21 Jun 2020 22:06:37: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sun, 21 Jun 2020 22:06:37: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:38: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:38: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:38: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:38: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:06:38: #2 alternative fragment length(s) may be 2,35 bps INFO @ Sun, 21 Jun 2020 22:06:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.20_model.r WARNING @ Sun, 21 Jun 2020 22:06:38: #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 22:06:38: #2 You may need to consider one of the other alternative d(s): 2,35 WARNING @ Sun, 21 Jun 2020 22:06:38: #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 22:06:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:06:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.05_summits.bed INFO @ Sun, 21 Jun 2020 22:06:58: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:06:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:07:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:07:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:07:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.10_summits.bed INFO @ Sun, 21 Jun 2020 22:07:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:07:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:07:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:07:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:07:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343120/SRX5343120.20_summits.bed INFO @ Sun, 21 Jun 2020 22:07:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling