Job ID = 6459314 SRX = SRX6685749 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:09:46 prefetch.2.10.7: 1) Downloading 'SRR9937042'... 2020-06-21T13:09:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:17:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:17:47 prefetch.2.10.7: 1) 'SRR9937042' was downloaded successfully 2020-06-21T13:17:47 prefetch.2.10.7: 'SRR9937042' has 0 unresolved dependencies Read 43050791 spots for SRR9937042/SRR9937042.sra Written 43050791 spots for SRR9937042/SRR9937042.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: 00:16:10 43050791 reads; of these: 43050791 (100.00%) were unpaired; of these: 10030072 (23.30%) aligned 0 times 22524473 (52.32%) aligned exactly 1 time 10496246 (24.38%) aligned >1 times 76.70% overall alignment rate Time searching: 00:16:10 Overall time: 00:16:10 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] 12720555 / 33020719 = 0.3852 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 22:46:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.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 22:46:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:46:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:46:18: 1000000 INFO @ Sun, 21 Jun 2020 22:46:25: 2000000 INFO @ Sun, 21 Jun 2020 22:46:31: 3000000 INFO @ Sun, 21 Jun 2020 22:46:37: 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 22:46:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.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 22:46:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:46:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:46:44: 5000000 INFO @ Sun, 21 Jun 2020 22:46:49: 1000000 INFO @ Sun, 21 Jun 2020 22:46:51: 6000000 INFO @ Sun, 21 Jun 2020 22:46:56: 2000000 INFO @ Sun, 21 Jun 2020 22:46:57: 7000000 INFO @ Sun, 21 Jun 2020 22:47:03: 3000000 INFO @ Sun, 21 Jun 2020 22:47:04: 8000000 INFO @ Sun, 21 Jun 2020 22:47:10: 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 22:47:11: 9000000 INFO @ Sun, 21 Jun 2020 22:47:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.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 22:47:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:47:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:47:17: 5000000 INFO @ Sun, 21 Jun 2020 22:47:19: 10000000 INFO @ Sun, 21 Jun 2020 22:47:19: 1000000 INFO @ Sun, 21 Jun 2020 22:47:24: 6000000 INFO @ Sun, 21 Jun 2020 22:47:26: 11000000 INFO @ Sun, 21 Jun 2020 22:47:27: 2000000 INFO @ Sun, 21 Jun 2020 22:47:31: 7000000 INFO @ Sun, 21 Jun 2020 22:47:33: 12000000 INFO @ Sun, 21 Jun 2020 22:47:34: 3000000 INFO @ Sun, 21 Jun 2020 22:47:38: 8000000 INFO @ Sun, 21 Jun 2020 22:47:40: 13000000 INFO @ Sun, 21 Jun 2020 22:47:41: 4000000 INFO @ Sun, 21 Jun 2020 22:47:45: 9000000 INFO @ Sun, 21 Jun 2020 22:47:47: 14000000 INFO @ Sun, 21 Jun 2020 22:47:48: 5000000 INFO @ Sun, 21 Jun 2020 22:47:52: 10000000 INFO @ Sun, 21 Jun 2020 22:47:54: 15000000 INFO @ Sun, 21 Jun 2020 22:47:55: 6000000 INFO @ Sun, 21 Jun 2020 22:48:00: 11000000 INFO @ Sun, 21 Jun 2020 22:48:01: 16000000 INFO @ Sun, 21 Jun 2020 22:48:02: 7000000 INFO @ Sun, 21 Jun 2020 22:48:07: 12000000 INFO @ Sun, 21 Jun 2020 22:48:08: 17000000 INFO @ Sun, 21 Jun 2020 22:48:09: 8000000 INFO @ Sun, 21 Jun 2020 22:48:14: 13000000 INFO @ Sun, 21 Jun 2020 22:48:16: 18000000 INFO @ Sun, 21 Jun 2020 22:48:16: 9000000 INFO @ Sun, 21 Jun 2020 22:48:21: 14000000 INFO @ Sun, 21 Jun 2020 22:48:23: 19000000 INFO @ Sun, 21 Jun 2020 22:48:23: 10000000 INFO @ Sun, 21 Jun 2020 22:48:28: 15000000 INFO @ Sun, 21 Jun 2020 22:48:30: 20000000 INFO @ Sun, 21 Jun 2020 22:48:30: 11000000 INFO @ Sun, 21 Jun 2020 22:48:32: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:48:32: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:48:32: #1 total tags in treatment: 20300164 INFO @ Sun, 21 Jun 2020 22:48:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:48:32: #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 22:48:33: #1 tags after filtering in treatment: 20300080 INFO @ Sun, 21 Jun 2020 22:48:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:48:33: #1 finished! INFO @ Sun, 21 Jun 2020 22:48:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:48:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:48:34: #2 number of paired peaks: 2448 INFO @ Sun, 21 Jun 2020 22:48:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:48:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:48:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:48:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:48:34: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 22:48:34: #2 alternative fragment length(s) may be 2,77 bps INFO @ Sun, 21 Jun 2020 22:48:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.05_model.r WARNING @ Sun, 21 Jun 2020 22:48:34: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:48:34: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Sun, 21 Jun 2020 22:48:34: #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 22:48:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:48:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:48:35: 16000000 INFO @ Sun, 21 Jun 2020 22:48:37: 12000000 INFO @ Sun, 21 Jun 2020 22:48:43: 17000000 INFO @ Sun, 21 Jun 2020 22:48:44: 13000000 INFO @ Sun, 21 Jun 2020 22:48:50: 18000000 INFO @ Sun, 21 Jun 2020 22:48:51: 14000000 INFO @ Sun, 21 Jun 2020 22:48:57: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:48:58: 15000000 INFO @ Sun, 21 Jun 2020 22:49:04: 20000000 INFO @ Sun, 21 Jun 2020 22:49:05: 16000000 INFO @ Sun, 21 Jun 2020 22:49:07: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:49:07: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:49:07: #1 total tags in treatment: 20300164 INFO @ Sun, 21 Jun 2020 22:49:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:49:07: #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 22:49:07: #1 tags after filtering in treatment: 20300080 INFO @ Sun, 21 Jun 2020 22:49:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:49:07: #1 finished! INFO @ Sun, 21 Jun 2020 22:49:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:49:09: #2 number of paired peaks: 2448 INFO @ Sun, 21 Jun 2020 22:49:09: start model_add_line... INFO @ Sun, 21 Jun 2020 22:49:09: start X-correlation... INFO @ Sun, 21 Jun 2020 22:49:09: end of X-cor INFO @ Sun, 21 Jun 2020 22:49:09: #2 finished! INFO @ Sun, 21 Jun 2020 22:49:09: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 22:49:09: #2 alternative fragment length(s) may be 2,77 bps INFO @ Sun, 21 Jun 2020 22:49:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.10_model.r WARNING @ Sun, 21 Jun 2020 22:49:09: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:49:09: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Sun, 21 Jun 2020 22:49:09: #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 22:49:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:49:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:49:12: 17000000 INFO @ Sun, 21 Jun 2020 22:49:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:49:19: 18000000 INFO @ Sun, 21 Jun 2020 22:49:25: 19000000 INFO @ Sun, 21 Jun 2020 22:49:31: 20000000 INFO @ Sun, 21 Jun 2020 22:49:33: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:49:33: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:49:33: #1 total tags in treatment: 20300164 INFO @ Sun, 21 Jun 2020 22:49:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:49:33: #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 22:49:34: #1 tags after filtering in treatment: 20300080 INFO @ Sun, 21 Jun 2020 22:49:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:49:34: #1 finished! INFO @ Sun, 21 Jun 2020 22:49:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:49:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:49:36: #2 number of paired peaks: 2448 INFO @ Sun, 21 Jun 2020 22:49:36: start model_add_line... INFO @ Sun, 21 Jun 2020 22:49:36: start X-correlation... INFO @ Sun, 21 Jun 2020 22:49:36: end of X-cor INFO @ Sun, 21 Jun 2020 22:49:36: #2 finished! INFO @ Sun, 21 Jun 2020 22:49:36: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 22:49:36: #2 alternative fragment length(s) may be 2,77 bps INFO @ Sun, 21 Jun 2020 22:49:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.20_model.r WARNING @ Sun, 21 Jun 2020 22:49:36: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:49:36: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Sun, 21 Jun 2020 22:49:36: #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 22:49:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:49:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:49:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:49:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:49:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.05_summits.bed INFO @ Sun, 21 Jun 2020 22:49:39: Done! pass1 - making usageList (751 chroms): 1 millis pass2 - checking and writing primary data (4690 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:49:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:50:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:50:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:50:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.10_summits.bed INFO @ Sun, 21 Jun 2020 22:50:15: Done! pass1 - making usageList (643 chroms): 1 millis pass2 - checking and writing primary data (2918 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:50:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:50:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:50:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:50:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685749/SRX6685749.20_summits.bed INFO @ Sun, 21 Jun 2020 22:50:42: Done! pass1 - making usageList (518 chroms): 1 millis pass2 - checking and writing primary data (1865 records, 4 fields): 17 millis CompletedMACS2peakCalling