Job ID = 6457512 SRX = SRX4664663 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:52:18 prefetch.2.10.7: 1) Downloading 'SRR7813090'... 2020-06-21T11:52:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:55:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:55:27 prefetch.2.10.7: 'SRR7813090' is valid 2020-06-21T11:55:27 prefetch.2.10.7: 1) 'SRR7813090' was downloaded successfully Read 20110391 spots for SRR7813090/SRR7813090.sra Written 20110391 spots for SRR7813090/SRR7813090.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: 00:06:36 20110391 reads; of these: 20110391 (100.00%) were unpaired; of these: 778125 (3.87%) aligned 0 times 13271721 (65.99%) aligned exactly 1 time 6060545 (30.14%) aligned >1 times 96.13% overall alignment rate Time searching: 00:06:36 Overall time: 00:06:36 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 8 files... [bam_rmdupse_core] 3271367 / 19332266 = 0.1692 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 21:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.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 21:07:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:07:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:44: 1000000 INFO @ Sun, 21 Jun 2020 21:07:50: 2000000 INFO @ Sun, 21 Jun 2020 21:07:55: 3000000 INFO @ Sun, 21 Jun 2020 21:08:00: 4000000 INFO @ Sun, 21 Jun 2020 21:08:05: 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 21:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.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 21:08:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:08:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:08:10: 6000000 INFO @ Sun, 21 Jun 2020 21:08:14: 1000000 INFO @ Sun, 21 Jun 2020 21:08:16: 7000000 INFO @ Sun, 21 Jun 2020 21:08:20: 2000000 INFO @ Sun, 21 Jun 2020 21:08:21: 8000000 INFO @ Sun, 21 Jun 2020 21:08:25: 3000000 INFO @ Sun, 21 Jun 2020 21:08:26: 9000000 INFO @ Sun, 21 Jun 2020 21:08:31: 4000000 INFO @ Sun, 21 Jun 2020 21:08:31: 10000000 INFO @ Sun, 21 Jun 2020 21:08:36: 5000000 INFO @ Sun, 21 Jun 2020 21:08:37: 11000000 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 21:08:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.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 21:08:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:08:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:08:41: 6000000 INFO @ Sun, 21 Jun 2020 21:08:42: 12000000 INFO @ Sun, 21 Jun 2020 21:08:45: 1000000 INFO @ Sun, 21 Jun 2020 21:08:47: 7000000 INFO @ Sun, 21 Jun 2020 21:08:48: 13000000 INFO @ Sun, 21 Jun 2020 21:08:50: 2000000 INFO @ Sun, 21 Jun 2020 21:08:52: 8000000 INFO @ Sun, 21 Jun 2020 21:08:53: 14000000 INFO @ Sun, 21 Jun 2020 21:08:56: 3000000 INFO @ Sun, 21 Jun 2020 21:08:58: 9000000 INFO @ Sun, 21 Jun 2020 21:08:59: 15000000 INFO @ Sun, 21 Jun 2020 21:09:02: 4000000 INFO @ Sun, 21 Jun 2020 21:09:03: 10000000 INFO @ Sun, 21 Jun 2020 21:09:04: 16000000 INFO @ Sun, 21 Jun 2020 21:09:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:09:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:09:05: #1 total tags in treatment: 16060899 INFO @ Sun, 21 Jun 2020 21:09:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:09:05: #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 21:09:05: #1 tags after filtering in treatment: 16060819 INFO @ Sun, 21 Jun 2020 21:09:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:09:05: #1 finished! INFO @ Sun, 21 Jun 2020 21:09:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:09:07: #2 number of paired peaks: 1538 INFO @ Sun, 21 Jun 2020 21:09:07: start model_add_line... INFO @ Sun, 21 Jun 2020 21:09:07: start X-correlation... INFO @ Sun, 21 Jun 2020 21:09:07: end of X-cor INFO @ Sun, 21 Jun 2020 21:09:07: #2 finished! INFO @ Sun, 21 Jun 2020 21:09:07: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 21:09:07: #2 alternative fragment length(s) may be 3,85,100,589 bps INFO @ Sun, 21 Jun 2020 21:09:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.05_model.r WARNING @ Sun, 21 Jun 2020 21:09:07: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:09:07: #2 You may need to consider one of the other alternative d(s): 3,85,100,589 WARNING @ Sun, 21 Jun 2020 21:09:07: #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 21:09:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:09:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:09:07: 5000000 INFO @ Sun, 21 Jun 2020 21:09:09: 11000000 INFO @ Sun, 21 Jun 2020 21:09:13: 6000000 INFO @ Sun, 21 Jun 2020 21:09:14: 12000000 INFO @ Sun, 21 Jun 2020 21:09:18: 7000000 INFO @ Sun, 21 Jun 2020 21:09:20: 13000000 INFO @ Sun, 21 Jun 2020 21:09:24: 8000000 INFO @ Sun, 21 Jun 2020 21:09:26: 14000000 INFO @ Sun, 21 Jun 2020 21:09:30: 9000000 INFO @ Sun, 21 Jun 2020 21:09:31: 15000000 INFO @ Sun, 21 Jun 2020 21:09:35: 10000000 INFO @ Sun, 21 Jun 2020 21:09:37: 16000000 INFO @ Sun, 21 Jun 2020 21:09:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:09:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:09:38: #1 total tags in treatment: 16060899 INFO @ Sun, 21 Jun 2020 21:09:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:09:38: #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 21:09:38: #1 tags after filtering in treatment: 16060819 INFO @ Sun, 21 Jun 2020 21:09:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:09:38: #1 finished! INFO @ Sun, 21 Jun 2020 21:09:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:09:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:09:40: #2 number of paired peaks: 1538 INFO @ Sun, 21 Jun 2020 21:09:40: start model_add_line... INFO @ Sun, 21 Jun 2020 21:09:40: start X-correlation... INFO @ Sun, 21 Jun 2020 21:09:40: end of X-cor INFO @ Sun, 21 Jun 2020 21:09:40: #2 finished! INFO @ Sun, 21 Jun 2020 21:09:40: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 21:09:40: #2 alternative fragment length(s) may be 3,85,100,589 bps INFO @ Sun, 21 Jun 2020 21:09:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.10_model.r WARNING @ Sun, 21 Jun 2020 21:09:40: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:09:40: #2 You may need to consider one of the other alternative d(s): 3,85,100,589 WARNING @ Sun, 21 Jun 2020 21:09:40: #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 21:09:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:09:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:09:41: 11000000 INFO @ Sun, 21 Jun 2020 21:09:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:09:47: 12000000 INFO @ Sun, 21 Jun 2020 21:09:52: 13000000 INFO @ Sun, 21 Jun 2020 21:09:58: 14000000 INFO @ Sun, 21 Jun 2020 21:10:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:10:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:10:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.05_summits.bed INFO @ Sun, 21 Jun 2020 21:10:03: Done! pass1 - making usageList (593 chroms): 1 millis pass2 - checking and writing primary data (4577 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:10:04: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:10:09: 16000000 INFO @ Sun, 21 Jun 2020 21:10:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:10:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:10:10: #1 total tags in treatment: 16060899 INFO @ Sun, 21 Jun 2020 21:10:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:10:10: #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 21:10:10: #1 tags after filtering in treatment: 16060819 INFO @ Sun, 21 Jun 2020 21:10:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:10:10: #1 finished! INFO @ Sun, 21 Jun 2020 21:10:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:10:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:10:12: #2 number of paired peaks: 1538 INFO @ Sun, 21 Jun 2020 21:10:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:10:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:10:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:10:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:10:12: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 21:10:12: #2 alternative fragment length(s) may be 3,85,100,589 bps INFO @ Sun, 21 Jun 2020 21:10:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.20_model.r WARNING @ Sun, 21 Jun 2020 21:10:12: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:10:12: #2 You may need to consider one of the other alternative d(s): 3,85,100,589 WARNING @ Sun, 21 Jun 2020 21:10:12: #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 21:10:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:10:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:10:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:10:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:10:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:10:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.10_summits.bed INFO @ Sun, 21 Jun 2020 21:10:36: Done! pass1 - making usageList (527 chroms): 1 millis pass2 - checking and writing primary data (2790 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:10:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:11:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:11:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:11:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664663/SRX4664663.20_summits.bed INFO @ Sun, 21 Jun 2020 21:11:08: Done! pass1 - making usageList (437 chroms): 1 millis pass2 - checking and writing primary data (1642 records, 4 fields): 15 millis CompletedMACS2peakCalling