Job ID = 6456155 SRX = SRX3270981 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:41:38 prefetch.2.10.7: 1) Downloading 'SRR6159392'... 2020-06-21T10:41:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:43:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:43:23 prefetch.2.10.7: 'SRR6159392' is valid 2020-06-21T10:43:23 prefetch.2.10.7: 1) 'SRR6159392' was downloaded successfully Read 11691113 spots for SRR6159392/SRR6159392.sra Written 11691113 spots for SRR6159392/SRR6159392.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: 00:02:50 11691113 reads; of these: 11691113 (100.00%) were unpaired; of these: 877785 (7.51%) aligned 0 times 6926597 (59.25%) aligned exactly 1 time 3886731 (33.25%) aligned >1 times 92.49% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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_rmdupse_core] 3137761 / 10813328 = 0.2902 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 19:49:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.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 19:49:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:16: 1000000 INFO @ Sun, 21 Jun 2020 19:49:21: 2000000 INFO @ Sun, 21 Jun 2020 19:49:26: 3000000 INFO @ Sun, 21 Jun 2020 19:49:31: 4000000 INFO @ Sun, 21 Jun 2020 19:49:36: 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 19:49:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.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 19:49:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:41: 6000000 INFO @ Sun, 21 Jun 2020 19:49:46: 1000000 INFO @ Sun, 21 Jun 2020 19:49:47: 7000000 INFO @ Sun, 21 Jun 2020 19:49:51: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 19:49:51: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 19:49:51: #1 total tags in treatment: 7675567 INFO @ Sun, 21 Jun 2020 19:49:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:51: #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 19:49:51: #1 tags after filtering in treatment: 7675564 INFO @ Sun, 21 Jun 2020 19:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:52: #2 number of paired peaks: 1344 INFO @ Sun, 21 Jun 2020 19:49:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:52: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:49:52: #2 alternative fragment length(s) may be 3,39,581 bps INFO @ Sun, 21 Jun 2020 19:49:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.05_model.r WARNING @ Sun, 21 Jun 2020 19:49:52: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:49:52: #2 You may need to consider one of the other alternative d(s): 3,39,581 WARNING @ Sun, 21 Jun 2020 19:49:52: #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 19:49:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:49:52: 2000000 INFO @ Sun, 21 Jun 2020 19:49:57: 3000000 INFO @ Sun, 21 Jun 2020 19:50:02: 4000000 INFO @ Sun, 21 Jun 2020 19:50:08: 5000000 INFO @ Sun, 21 Jun 2020 19:50:08: #3 Call peaks for each chromosome... 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 19:50:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.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 19:50:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:13: 6000000 INFO @ Sun, 21 Jun 2020 19:50:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.05_summits.bed INFO @ Sun, 21 Jun 2020 19:50:15: Done! INFO @ Sun, 21 Jun 2020 19:50:17: 1000000 pass1 - making usageList (658 chroms): 2 millis pass2 - checking and writing primary data (2973 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:50:19: 7000000 INFO @ Sun, 21 Jun 2020 19:50:22: 2000000 INFO @ Sun, 21 Jun 2020 19:50:23: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 19:50:23: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 19:50:23: #1 total tags in treatment: 7675567 INFO @ Sun, 21 Jun 2020 19:50:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:23: #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 19:50:23: #1 tags after filtering in treatment: 7675564 INFO @ Sun, 21 Jun 2020 19:50:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:24: #2 number of paired peaks: 1344 INFO @ Sun, 21 Jun 2020 19:50:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:24: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:50:24: #2 alternative fragment length(s) may be 3,39,581 bps INFO @ Sun, 21 Jun 2020 19:50:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.10_model.r WARNING @ Sun, 21 Jun 2020 19:50:24: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:50:24: #2 You may need to consider one of the other alternative d(s): 3,39,581 WARNING @ Sun, 21 Jun 2020 19:50:24: #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 19:50:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:27: 3000000 INFO @ Sun, 21 Jun 2020 19:50:33: 4000000 INFO @ Sun, 21 Jun 2020 19:50:38: 5000000 INFO @ Sun, 21 Jun 2020 19:50:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:43: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:50:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.10_summits.bed INFO @ Sun, 21 Jun 2020 19:50:48: Done! pass1 - making usageList (530 chroms): 1 millis pass2 - checking and writing primary data (1949 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:50:49: 7000000 INFO @ Sun, 21 Jun 2020 19:50:52: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 19:50:52: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 19:50:52: #1 total tags in treatment: 7675567 INFO @ Sun, 21 Jun 2020 19:50:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:52: #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 19:50:53: #1 tags after filtering in treatment: 7675564 INFO @ Sun, 21 Jun 2020 19:50:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:53: #2 number of paired peaks: 1344 INFO @ Sun, 21 Jun 2020 19:50:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:53: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:50:53: #2 alternative fragment length(s) may be 3,39,581 bps INFO @ Sun, 21 Jun 2020 19:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.20_model.r WARNING @ Sun, 21 Jun 2020 19:50:54: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:50:54: #2 You may need to consider one of the other alternative d(s): 3,39,581 WARNING @ Sun, 21 Jun 2020 19:50:54: #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 19:50:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:51:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270981/SRX3270981.20_summits.bed INFO @ Sun, 21 Jun 2020 19:51:18: Done! pass1 - making usageList (229 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 8 millis CompletedMACS2peakCalling