Job ID = 6458582 SRX = SRX5343118 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:33:04 prefetch.2.10.7: 1) Downloading 'SRR8540818'... 2020-06-21T12:33:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:35:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:35:38 prefetch.2.10.7: 1) 'SRR8540818' was downloaded successfully 2020-06-21T12:35:38 prefetch.2.10.7: 'SRR8540818' has 0 unresolved dependencies Read 26547410 spots for SRR8540818/SRR8540818.sra Written 26547410 spots for SRR8540818/SRR8540818.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: 00:08:59 26547410 reads; of these: 26547410 (100.00%) were unpaired; of these: 1474079 (5.55%) aligned 0 times 17237323 (64.93%) aligned exactly 1 time 7836008 (29.52%) aligned >1 times 94.45% overall alignment rate Time searching: 00:08:59 Overall time: 00:08:59 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 12 files... [bam_rmdupse_core] 3780301 / 25073331 = 0.1508 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 21:54:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.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 21:54:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:14: 1000000 INFO @ Sun, 21 Jun 2020 21:54:20: 2000000 INFO @ Sun, 21 Jun 2020 21:54:25: 3000000 INFO @ Sun, 21 Jun 2020 21:54:31: 4000000 INFO @ Sun, 21 Jun 2020 21:54:36: 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 21:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.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 21:54:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:42: 6000000 INFO @ Sun, 21 Jun 2020 21:54:45: 1000000 INFO @ Sun, 21 Jun 2020 21:54:48: 7000000 INFO @ Sun, 21 Jun 2020 21:54:51: 2000000 INFO @ Sun, 21 Jun 2020 21:54:54: 8000000 INFO @ Sun, 21 Jun 2020 21:54:57: 3000000 INFO @ Sun, 21 Jun 2020 21:55:00: 9000000 INFO @ Sun, 21 Jun 2020 21:55:03: 4000000 INFO @ Sun, 21 Jun 2020 21:55:06: 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 21:55:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.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 21:55:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:09: 5000000 INFO @ Sun, 21 Jun 2020 21:55:12: 11000000 INFO @ Sun, 21 Jun 2020 21:55:15: 1000000 INFO @ Sun, 21 Jun 2020 21:55:15: 6000000 INFO @ Sun, 21 Jun 2020 21:55:19: 12000000 INFO @ Sun, 21 Jun 2020 21:55:21: 2000000 INFO @ Sun, 21 Jun 2020 21:55:21: 7000000 INFO @ Sun, 21 Jun 2020 21:55:25: 13000000 INFO @ Sun, 21 Jun 2020 21:55:27: 3000000 INFO @ Sun, 21 Jun 2020 21:55:27: 8000000 INFO @ Sun, 21 Jun 2020 21:55:31: 14000000 INFO @ Sun, 21 Jun 2020 21:55:33: 4000000 INFO @ Sun, 21 Jun 2020 21:55:33: 9000000 INFO @ Sun, 21 Jun 2020 21:55:37: 15000000 INFO @ Sun, 21 Jun 2020 21:55:39: 5000000 INFO @ Sun, 21 Jun 2020 21:55:39: 10000000 INFO @ Sun, 21 Jun 2020 21:55:43: 16000000 INFO @ Sun, 21 Jun 2020 21:55:46: 6000000 INFO @ Sun, 21 Jun 2020 21:55:46: 11000000 INFO @ Sun, 21 Jun 2020 21:55:49: 17000000 INFO @ Sun, 21 Jun 2020 21:55:52: 7000000 INFO @ Sun, 21 Jun 2020 21:55:52: 12000000 INFO @ Sun, 21 Jun 2020 21:55:55: 18000000 INFO @ Sun, 21 Jun 2020 21:55:58: 8000000 INFO @ Sun, 21 Jun 2020 21:55:58: 13000000 INFO @ Sun, 21 Jun 2020 21:56:02: 19000000 INFO @ Sun, 21 Jun 2020 21:56:04: 9000000 INFO @ Sun, 21 Jun 2020 21:56:04: 14000000 INFO @ Sun, 21 Jun 2020 21:56:08: 20000000 INFO @ Sun, 21 Jun 2020 21:56:11: 15000000 INFO @ Sun, 21 Jun 2020 21:56:11: 10000000 INFO @ Sun, 21 Jun 2020 21:56:15: 21000000 INFO @ Sun, 21 Jun 2020 21:56:17: 16000000 INFO @ Sun, 21 Jun 2020 21:56:17: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:56:17: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:56:17: #1 total tags in treatment: 21293030 INFO @ Sun, 21 Jun 2020 21:56:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:17: #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 21:56:17: 11000000 INFO @ Sun, 21 Jun 2020 21:56:17: #1 tags after filtering in treatment: 21293029 INFO @ Sun, 21 Jun 2020 21:56:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:19: #2 number of paired peaks: 285 WARNING @ Sun, 21 Jun 2020 21:56:19: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 21 Jun 2020 21:56:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:19: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 21:56:19: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 21 Jun 2020 21:56:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.05_model.r WARNING @ Sun, 21 Jun 2020 21:56:19: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:56:19: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 21 Jun 2020 21:56:19: #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 21:56:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:23: 17000000 INFO @ Sun, 21 Jun 2020 21:56:24: 12000000 INFO @ Sun, 21 Jun 2020 21:56:29: 18000000 INFO @ Sun, 21 Jun 2020 21:56:30: 13000000 INFO @ Sun, 21 Jun 2020 21:56:36: 19000000 INFO @ Sun, 21 Jun 2020 21:56:36: 14000000 INFO @ Sun, 21 Jun 2020 21:56:42: 20000000 INFO @ Sun, 21 Jun 2020 21:56:43: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:56:48: 21000000 INFO @ Sun, 21 Jun 2020 21:56:49: 16000000 INFO @ Sun, 21 Jun 2020 21:56:50: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:56:50: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:56:50: #1 total tags in treatment: 21293030 INFO @ Sun, 21 Jun 2020 21:56:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:50: #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 21:56:51: #1 tags after filtering in treatment: 21293029 INFO @ Sun, 21 Jun 2020 21:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:51: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:52: #2 number of paired peaks: 285 WARNING @ Sun, 21 Jun 2020 21:56:52: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 21 Jun 2020 21:56:52: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:52: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:52: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:52: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:52: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 21:56:52: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 21 Jun 2020 21:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.10_model.r WARNING @ Sun, 21 Jun 2020 21:56:52: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:56:52: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 21 Jun 2020 21:56:52: #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 21:56:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:55: 17000000 INFO @ Sun, 21 Jun 2020 21:56:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:57:01: 18000000 INFO @ Sun, 21 Jun 2020 21:57:07: 19000000 INFO @ Sun, 21 Jun 2020 21:57:13: 20000000 INFO @ Sun, 21 Jun 2020 21:57:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.05_summits.bed INFO @ Sun, 21 Jun 2020 21:57:15: Done! pass1 - making usageList (711 chroms): 1 millis pass2 - checking and writing primary data (2483 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:57:20: 21000000 INFO @ Sun, 21 Jun 2020 21:57:22: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:57:22: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:57:22: #1 total tags in treatment: 21293030 INFO @ Sun, 21 Jun 2020 21:57:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:57:22: #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 21:57:22: #1 tags after filtering in treatment: 21293029 INFO @ Sun, 21 Jun 2020 21:57:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:57:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:57:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:57:23: #2 number of paired peaks: 285 WARNING @ Sun, 21 Jun 2020 21:57:23: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 21 Jun 2020 21:57:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:57:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:57:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:57:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:57:24: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 21:57:24: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 21 Jun 2020 21:57:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.20_model.r WARNING @ Sun, 21 Jun 2020 21:57:24: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:57:24: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 21 Jun 2020 21:57:24: #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 21:57:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:57:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:57:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:57:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.10_summits.bed INFO @ Sun, 21 Jun 2020 21:57:50: Done! pass1 - making usageList (546 chroms): 1 millis pass2 - checking and writing primary data (1779 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:58:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:58:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:58:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:58:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343118/SRX5343118.20_summits.bed INFO @ Sun, 21 Jun 2020 21:58:20: Done! pass1 - making usageList (333 chroms): 1 millis pass2 - checking and writing primary data (686 records, 4 fields): 10 millis CompletedMACS2peakCalling