Job ID = 6454497 SRX = SRX2165281 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:17:09 prefetch.2.10.7: 1) Downloading 'SRR4244791'... 2020-06-21T09:17:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:20:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:20:42 prefetch.2.10.7: 'SRR4244791' is valid 2020-06-21T09:20:42 prefetch.2.10.7: 1) 'SRR4244791' was downloaded successfully Read 12937507 spots for SRR4244791/SRR4244791.sra Written 12937507 spots for SRR4244791/SRR4244791.sra 2020-06-21T09:21:31 prefetch.2.10.7: 1) Downloading 'SRR4244792'... 2020-06-21T09:21:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:25:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:25:52 prefetch.2.10.7: 1) 'SRR4244792' was downloaded successfully Read 16182114 spots for SRR4244792/SRR4244792.sra Written 16182114 spots for SRR4244792/SRR4244792.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: 00:08:53 29119621 reads; of these: 29119621 (100.00%) were unpaired; of these: 5766957 (19.80%) aligned 0 times 17474546 (60.01%) aligned exactly 1 time 5878118 (20.19%) aligned >1 times 80.20% overall alignment rate Time searching: 00:08:54 Overall time: 00:08:54 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] 9867673 / 23352664 = 0.4226 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 18:42:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.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 18:42:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:50: 1000000 INFO @ Sun, 21 Jun 2020 18:42:57: 2000000 INFO @ Sun, 21 Jun 2020 18:43:04: 3000000 INFO @ Sun, 21 Jun 2020 18:43:10: 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 18:43:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.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 18:43:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:17: 5000000 INFO @ Sun, 21 Jun 2020 18:43:21: 1000000 INFO @ Sun, 21 Jun 2020 18:43:25: 6000000 INFO @ Sun, 21 Jun 2020 18:43:29: 2000000 INFO @ Sun, 21 Jun 2020 18:43:32: 7000000 INFO @ Sun, 21 Jun 2020 18:43:36: 3000000 INFO @ Sun, 21 Jun 2020 18:43:40: 8000000 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 18:43:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.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 18:43:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:44: 4000000 INFO @ Sun, 21 Jun 2020 18:43:47: 9000000 INFO @ Sun, 21 Jun 2020 18:43:52: 5000000 INFO @ Sun, 21 Jun 2020 18:43:52: 1000000 INFO @ Sun, 21 Jun 2020 18:43:55: 10000000 INFO @ Sun, 21 Jun 2020 18:43:59: 6000000 INFO @ Sun, 21 Jun 2020 18:43:59: 2000000 INFO @ Sun, 21 Jun 2020 18:44:03: 11000000 INFO @ Sun, 21 Jun 2020 18:44:07: 7000000 INFO @ Sun, 21 Jun 2020 18:44:07: 3000000 INFO @ Sun, 21 Jun 2020 18:44:11: 12000000 INFO @ Sun, 21 Jun 2020 18:44:14: 8000000 INFO @ Sun, 21 Jun 2020 18:44:15: 4000000 INFO @ Sun, 21 Jun 2020 18:44:19: 13000000 INFO @ Sun, 21 Jun 2020 18:44:22: 9000000 INFO @ Sun, 21 Jun 2020 18:44:22: 5000000 INFO @ Sun, 21 Jun 2020 18:44:22: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:44:22: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:44:22: #1 total tags in treatment: 13484991 INFO @ Sun, 21 Jun 2020 18:44:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:22: #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 18:44:23: #1 tags after filtering in treatment: 13484991 INFO @ Sun, 21 Jun 2020 18:44:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:24: #2 number of paired peaks: 1074 INFO @ Sun, 21 Jun 2020 18:44:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:24: #2 predicted fragment length is 110 bps INFO @ Sun, 21 Jun 2020 18:44:24: #2 alternative fragment length(s) may be 110 bps INFO @ Sun, 21 Jun 2020 18:44:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.05_model.r WARNING @ Sun, 21 Jun 2020 18:44:24: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:44:24: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Sun, 21 Jun 2020 18:44:24: #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 18:44:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:29: 10000000 INFO @ Sun, 21 Jun 2020 18:44:30: 6000000 INFO @ Sun, 21 Jun 2020 18:44:37: 11000000 INFO @ Sun, 21 Jun 2020 18:44:37: 7000000 INFO @ Sun, 21 Jun 2020 18:44:45: 12000000 INFO @ Sun, 21 Jun 2020 18:44:45: 8000000 INFO @ Sun, 21 Jun 2020 18:44:52: 9000000 INFO @ Sun, 21 Jun 2020 18:44:52: 13000000 INFO @ Sun, 21 Jun 2020 18:44:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:56: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:44:56: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:44:56: #1 total tags in treatment: 13484991 INFO @ Sun, 21 Jun 2020 18:44:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:56: #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 18:44:57: #1 tags after filtering in treatment: 13484991 INFO @ Sun, 21 Jun 2020 18:44:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:57: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:58: #2 number of paired peaks: 1074 INFO @ Sun, 21 Jun 2020 18:44:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:58: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:58: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:58: #2 predicted fragment length is 110 bps INFO @ Sun, 21 Jun 2020 18:44:58: #2 alternative fragment length(s) may be 110 bps INFO @ Sun, 21 Jun 2020 18:44:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.10_model.r WARNING @ Sun, 21 Jun 2020 18:44:58: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:44:58: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Sun, 21 Jun 2020 18:44:58: #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 18:44:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:59: 10000000 INFO @ Sun, 21 Jun 2020 18:45:06: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:45:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.05_summits.bed INFO @ Sun, 21 Jun 2020 18:45:12: Done! pass1 - making usageList (769 chroms): 1 millis pass2 - checking and writing primary data (5039 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:45:13: 12000000 INFO @ Sun, 21 Jun 2020 18:45:19: 13000000 INFO @ Sun, 21 Jun 2020 18:45:23: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:45:23: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:45:23: #1 total tags in treatment: 13484991 INFO @ Sun, 21 Jun 2020 18:45:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:23: #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 18:45:23: #1 tags after filtering in treatment: 13484991 INFO @ Sun, 21 Jun 2020 18:45:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:24: #2 number of paired peaks: 1074 INFO @ Sun, 21 Jun 2020 18:45:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:25: #2 predicted fragment length is 110 bps INFO @ Sun, 21 Jun 2020 18:45:25: #2 alternative fragment length(s) may be 110 bps INFO @ Sun, 21 Jun 2020 18:45:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.20_model.r WARNING @ Sun, 21 Jun 2020 18:45:25: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:25: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Sun, 21 Jun 2020 18:45:25: #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 18:45:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:45:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.10_summits.bed INFO @ Sun, 21 Jun 2020 18:45:44: Done! pass1 - making usageList (661 chroms): 1 millis pass2 - checking and writing primary data (3083 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:45:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165281/SRX2165281.20_summits.bed INFO @ Sun, 21 Jun 2020 18:46:11: Done! pass1 - making usageList (500 chroms): 2 millis pass2 - checking and writing primary data (1746 records, 4 fields): 17 millis CompletedMACS2peakCalling