Job ID = 6459584 SRX = SRX7158301 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:26:13 prefetch.2.10.7: 1) Downloading 'SRR10467047'... 2020-06-21T13:26:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:34:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:34:35 prefetch.2.10.7: 1) 'SRR10467047' was downloaded successfully 2020-06-21T13:34:35 prefetch.2.10.7: 'SRR10467047' has 0 unresolved dependencies Read 46504024 spots for SRR10467047/SRR10467047.sra Written 46504024 spots for SRR10467047/SRR10467047.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: 00:14:37 46504024 reads; of these: 46504024 (100.00%) were unpaired; of these: 1520357 (3.27%) aligned 0 times 40623528 (87.35%) aligned exactly 1 time 4360139 (9.38%) aligned >1 times 96.73% overall alignment rate Time searching: 00:14:37 Overall time: 00:14:37 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] 21732909 / 44983667 = 0.4831 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 23:01:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.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 23:01:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:01:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:02:00: 1000000 INFO @ Sun, 21 Jun 2020 23:02:06: 2000000 INFO @ Sun, 21 Jun 2020 23:02:11: 3000000 INFO @ Sun, 21 Jun 2020 23:02:17: 4000000 INFO @ Sun, 21 Jun 2020 23:02:22: 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 23:02:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.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 23:02:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:02:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:02:27: 6000000 INFO @ Sun, 21 Jun 2020 23:02:31: 1000000 INFO @ Sun, 21 Jun 2020 23:02:33: 7000000 INFO @ Sun, 21 Jun 2020 23:02:36: 2000000 INFO @ Sun, 21 Jun 2020 23:02:39: 8000000 INFO @ Sun, 21 Jun 2020 23:02:42: 3000000 INFO @ Sun, 21 Jun 2020 23:02:44: 9000000 INFO @ Sun, 21 Jun 2020 23:02:48: 4000000 INFO @ Sun, 21 Jun 2020 23:02:50: 10000000 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 23:02:53: 5000000 INFO @ Sun, 21 Jun 2020 23:02:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.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 23:02:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:02:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:02:56: 11000000 INFO @ Sun, 21 Jun 2020 23:02:59: 6000000 INFO @ Sun, 21 Jun 2020 23:03:01: 1000000 INFO @ Sun, 21 Jun 2020 23:03:01: 12000000 INFO @ Sun, 21 Jun 2020 23:03:05: 7000000 INFO @ Sun, 21 Jun 2020 23:03:07: 2000000 INFO @ Sun, 21 Jun 2020 23:03:07: 13000000 INFO @ Sun, 21 Jun 2020 23:03:11: 8000000 INFO @ Sun, 21 Jun 2020 23:03:12: 3000000 INFO @ Sun, 21 Jun 2020 23:03:13: 14000000 INFO @ Sun, 21 Jun 2020 23:03:16: 9000000 INFO @ Sun, 21 Jun 2020 23:03:18: 4000000 INFO @ Sun, 21 Jun 2020 23:03:19: 15000000 INFO @ Sun, 21 Jun 2020 23:03:22: 10000000 INFO @ Sun, 21 Jun 2020 23:03:24: 5000000 INFO @ Sun, 21 Jun 2020 23:03:24: 16000000 INFO @ Sun, 21 Jun 2020 23:03:28: 11000000 INFO @ Sun, 21 Jun 2020 23:03:30: 6000000 INFO @ Sun, 21 Jun 2020 23:03:30: 17000000 INFO @ Sun, 21 Jun 2020 23:03:33: 12000000 INFO @ Sun, 21 Jun 2020 23:03:35: 7000000 INFO @ Sun, 21 Jun 2020 23:03:36: 18000000 INFO @ Sun, 21 Jun 2020 23:03:39: 13000000 INFO @ Sun, 21 Jun 2020 23:03:41: 8000000 INFO @ Sun, 21 Jun 2020 23:03:42: 19000000 INFO @ Sun, 21 Jun 2020 23:03:45: 14000000 INFO @ Sun, 21 Jun 2020 23:03:46: 9000000 INFO @ Sun, 21 Jun 2020 23:03:48: 20000000 INFO @ Sun, 21 Jun 2020 23:03:50: 15000000 INFO @ Sun, 21 Jun 2020 23:03:52: 10000000 INFO @ Sun, 21 Jun 2020 23:03:53: 21000000 INFO @ Sun, 21 Jun 2020 23:03:56: 16000000 INFO @ Sun, 21 Jun 2020 23:03:58: 11000000 INFO @ Sun, 21 Jun 2020 23:03:59: 22000000 INFO @ Sun, 21 Jun 2020 23:04:02: 17000000 INFO @ Sun, 21 Jun 2020 23:04:03: 12000000 INFO @ Sun, 21 Jun 2020 23:04:05: 23000000 INFO @ Sun, 21 Jun 2020 23:04:07: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 23:04:07: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 23:04:07: #1 total tags in treatment: 23250758 INFO @ Sun, 21 Jun 2020 23:04:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:04:07: #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 23:04:07: #1 tags after filtering in treatment: 23250641 INFO @ Sun, 21 Jun 2020 23:04:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:04:07: #1 finished! INFO @ Sun, 21 Jun 2020 23:04:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:04:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:04:08: 18000000 INFO @ Sun, 21 Jun 2020 23:04:09: #2 number of paired peaks: 446 WARNING @ Sun, 21 Jun 2020 23:04:09: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Sun, 21 Jun 2020 23:04:09: start model_add_line... INFO @ Sun, 21 Jun 2020 23:04:09: 13000000 INFO @ Sun, 21 Jun 2020 23:04:09: start X-correlation... INFO @ Sun, 21 Jun 2020 23:04:09: end of X-cor INFO @ Sun, 21 Jun 2020 23:04:09: #2 finished! INFO @ Sun, 21 Jun 2020 23:04:09: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 23:04:09: #2 alternative fragment length(s) may be 2,85 bps INFO @ Sun, 21 Jun 2020 23:04:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.05_model.r WARNING @ Sun, 21 Jun 2020 23:04:09: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:04:09: #2 You may need to consider one of the other alternative d(s): 2,85 WARNING @ Sun, 21 Jun 2020 23:04:09: #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 23:04:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:04:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:04:14: 19000000 INFO @ Sun, 21 Jun 2020 23:04:15: 14000000 INFO @ Sun, 21 Jun 2020 23:04:20: 20000000 INFO @ Sun, 21 Jun 2020 23:04:20: 15000000 INFO @ Sun, 21 Jun 2020 23:04:25: 21000000 INFO @ Sun, 21 Jun 2020 23:04:26: 16000000 INFO @ Sun, 21 Jun 2020 23:04:31: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:04:32: 17000000 INFO @ Sun, 21 Jun 2020 23:04:36: 23000000 INFO @ Sun, 21 Jun 2020 23:04:37: 18000000 INFO @ Sun, 21 Jun 2020 23:04:38: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 23:04:38: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 23:04:38: #1 total tags in treatment: 23250758 INFO @ Sun, 21 Jun 2020 23:04:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:04:38: #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 23:04:39: #1 tags after filtering in treatment: 23250641 INFO @ Sun, 21 Jun 2020 23:04:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:04:39: #1 finished! INFO @ Sun, 21 Jun 2020 23:04:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:04:40: #2 number of paired peaks: 446 WARNING @ Sun, 21 Jun 2020 23:04:40: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Sun, 21 Jun 2020 23:04:40: start model_add_line... INFO @ Sun, 21 Jun 2020 23:04:40: start X-correlation... INFO @ Sun, 21 Jun 2020 23:04:40: end of X-cor INFO @ Sun, 21 Jun 2020 23:04:40: #2 finished! INFO @ Sun, 21 Jun 2020 23:04:40: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 23:04:40: #2 alternative fragment length(s) may be 2,85 bps INFO @ Sun, 21 Jun 2020 23:04:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.10_model.r WARNING @ Sun, 21 Jun 2020 23:04:40: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:04:40: #2 You may need to consider one of the other alternative d(s): 2,85 WARNING @ Sun, 21 Jun 2020 23:04:40: #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 23:04:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:04:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:04:43: 19000000 INFO @ Sun, 21 Jun 2020 23:04:48: 20000000 INFO @ Sun, 21 Jun 2020 23:04:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:04:54: 21000000 INFO @ Sun, 21 Jun 2020 23:04:59: 22000000 INFO @ Sun, 21 Jun 2020 23:05:04: 23000000 INFO @ Sun, 21 Jun 2020 23:05:06: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 23:05:06: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 23:05:06: #1 total tags in treatment: 23250758 INFO @ Sun, 21 Jun 2020 23:05:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:05:06: #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 23:05:06: #1 tags after filtering in treatment: 23250641 INFO @ Sun, 21 Jun 2020 23:05:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:05:06: #1 finished! INFO @ Sun, 21 Jun 2020 23:05:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:05:08: #2 number of paired peaks: 446 WARNING @ Sun, 21 Jun 2020 23:05:08: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Sun, 21 Jun 2020 23:05:08: start model_add_line... INFO @ Sun, 21 Jun 2020 23:05:08: start X-correlation... INFO @ Sun, 21 Jun 2020 23:05:08: end of X-cor INFO @ Sun, 21 Jun 2020 23:05:08: #2 finished! INFO @ Sun, 21 Jun 2020 23:05:08: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 23:05:08: #2 alternative fragment length(s) may be 2,85 bps INFO @ Sun, 21 Jun 2020 23:05:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.20_model.r WARNING @ Sun, 21 Jun 2020 23:05:08: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:05:08: #2 You may need to consider one of the other alternative d(s): 2,85 WARNING @ Sun, 21 Jun 2020 23:05:08: #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 23:05:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:05:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:05:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:05:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:05:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.05_summits.bed INFO @ Sun, 21 Jun 2020 23:05:12: Done! pass1 - making usageList (199 chroms): 2 millis pass2 - checking and writing primary data (5635 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:05:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:05:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:05:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:05:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.10_summits.bed INFO @ Sun, 21 Jun 2020 23:05:45: Done! pass1 - making usageList (134 chroms): 1 millis pass2 - checking and writing primary data (1800 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:05:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:06:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:06:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:06:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7158301/SRX7158301.20_summits.bed INFO @ Sun, 21 Jun 2020 23:06:13: Done! pass1 - making usageList (99 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 4 millis CompletedMACS2peakCalling