Job ID = 6454438 SRX = SRX2055966 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:06:09 prefetch.2.10.7: 1) Downloading 'SRR4069198'... 2020-06-21T09:06:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:13:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:13:40 prefetch.2.10.7: 1) 'SRR4069198' was downloaded successfully Read 25880670 spots for SRR4069198/SRR4069198.sra Written 25880670 spots for SRR4069198/SRR4069198.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: 00:08:08 25880670 reads; of these: 25880670 (100.00%) were unpaired; of these: 1227869 (4.74%) aligned 0 times 15508674 (59.92%) aligned exactly 1 time 9144127 (35.33%) aligned >1 times 95.26% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 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] 5021050 / 24652801 = 0.2037 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 18:28:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.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 18:28:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:28:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:28:18: 1000000 INFO @ Sun, 21 Jun 2020 18:28:24: 2000000 INFO @ Sun, 21 Jun 2020 18:28:29: 3000000 INFO @ Sun, 21 Jun 2020 18:28:35: 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 18:28:41: 5000000 INFO @ Sun, 21 Jun 2020 18:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.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 18:28:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:28:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:28:46: 6000000 INFO @ Sun, 21 Jun 2020 18:28:48: 1000000 INFO @ Sun, 21 Jun 2020 18:28:52: 7000000 INFO @ Sun, 21 Jun 2020 18:28:53: 2000000 INFO @ Sun, 21 Jun 2020 18:28:58: 8000000 INFO @ Sun, 21 Jun 2020 18:28:58: 3000000 INFO @ Sun, 21 Jun 2020 18:29:03: 4000000 INFO @ Sun, 21 Jun 2020 18:29:04: 9000000 INFO @ Sun, 21 Jun 2020 18:29:09: 5000000 INFO @ Sun, 21 Jun 2020 18:29:10: 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 18:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.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 18:29:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:29:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:29:14: 6000000 INFO @ Sun, 21 Jun 2020 18:29:16: 11000000 INFO @ Sun, 21 Jun 2020 18:29:18: 1000000 INFO @ Sun, 21 Jun 2020 18:29:19: 7000000 INFO @ Sun, 21 Jun 2020 18:29:21: 12000000 INFO @ Sun, 21 Jun 2020 18:29:23: 2000000 INFO @ Sun, 21 Jun 2020 18:29:24: 8000000 INFO @ Sun, 21 Jun 2020 18:29:27: 13000000 INFO @ Sun, 21 Jun 2020 18:29:28: 3000000 INFO @ Sun, 21 Jun 2020 18:29:29: 9000000 INFO @ Sun, 21 Jun 2020 18:29:33: 14000000 INFO @ Sun, 21 Jun 2020 18:29:34: 4000000 INFO @ Sun, 21 Jun 2020 18:29:35: 10000000 INFO @ Sun, 21 Jun 2020 18:29:39: 5000000 INFO @ Sun, 21 Jun 2020 18:29:39: 15000000 INFO @ Sun, 21 Jun 2020 18:29:40: 11000000 INFO @ Sun, 21 Jun 2020 18:29:44: 6000000 INFO @ Sun, 21 Jun 2020 18:29:45: 12000000 INFO @ Sun, 21 Jun 2020 18:29:45: 16000000 INFO @ Sun, 21 Jun 2020 18:29:49: 7000000 INFO @ Sun, 21 Jun 2020 18:29:50: 13000000 INFO @ Sun, 21 Jun 2020 18:29:51: 17000000 INFO @ Sun, 21 Jun 2020 18:29:55: 8000000 INFO @ Sun, 21 Jun 2020 18:29:55: 14000000 INFO @ Sun, 21 Jun 2020 18:29:57: 18000000 INFO @ Sun, 21 Jun 2020 18:30:00: 9000000 INFO @ Sun, 21 Jun 2020 18:30:01: 15000000 INFO @ Sun, 21 Jun 2020 18:30:03: 19000000 INFO @ Sun, 21 Jun 2020 18:30:05: 10000000 INFO @ Sun, 21 Jun 2020 18:30:06: 16000000 INFO @ Sun, 21 Jun 2020 18:30:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:30:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:30:07: #1 total tags in treatment: 19631751 INFO @ Sun, 21 Jun 2020 18:30:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:30:07: #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 18:30:08: #1 tags after filtering in treatment: 19631688 INFO @ Sun, 21 Jun 2020 18:30:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:30:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:30:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:30:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:30:09: #2 number of paired peaks: 1766 INFO @ Sun, 21 Jun 2020 18:30:09: start model_add_line... INFO @ Sun, 21 Jun 2020 18:30:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:30:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:30:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:30:09: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:30:09: #2 alternative fragment length(s) may be 1,47 bps INFO @ Sun, 21 Jun 2020 18:30:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.05_model.r WARNING @ Sun, 21 Jun 2020 18:30:09: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:30:09: #2 You may need to consider one of the other alternative d(s): 1,47 WARNING @ Sun, 21 Jun 2020 18:30:09: #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 18:30:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:30:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:30:10: 11000000 INFO @ Sun, 21 Jun 2020 18:30:12: 17000000 INFO @ Sun, 21 Jun 2020 18:30:16: 12000000 INFO @ Sun, 21 Jun 2020 18:30:17: 18000000 INFO @ Sun, 21 Jun 2020 18:30:21: 13000000 INFO @ Sun, 21 Jun 2020 18:30:22: 19000000 INFO @ Sun, 21 Jun 2020 18:30:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:30:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:30:25: #1 total tags in treatment: 19631751 INFO @ Sun, 21 Jun 2020 18:30:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:30:25: #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 18:30:26: 14000000 INFO @ Sun, 21 Jun 2020 18:30:26: #1 tags after filtering in treatment: 19631688 INFO @ Sun, 21 Jun 2020 18:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:30:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:30:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:30:27: #2 number of paired peaks: 1766 INFO @ Sun, 21 Jun 2020 18:30:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:30:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:30:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:30:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:30:28: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:30:28: #2 alternative fragment length(s) may be 1,47 bps INFO @ Sun, 21 Jun 2020 18:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.10_model.r WARNING @ Sun, 21 Jun 2020 18:30:28: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:30:28: #2 You may need to consider one of the other alternative d(s): 1,47 WARNING @ Sun, 21 Jun 2020 18:30:28: #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 18:30:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:30:31: 15000000 INFO @ Sun, 21 Jun 2020 18:30:36: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:30:41: 17000000 INFO @ Sun, 21 Jun 2020 18:30:46: 18000000 INFO @ Sun, 21 Jun 2020 18:30:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:30:51: 19000000 INFO @ Sun, 21 Jun 2020 18:30:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:30:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:30:54: #1 total tags in treatment: 19631751 INFO @ Sun, 21 Jun 2020 18:30:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:30:54: #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 18:30:55: #1 tags after filtering in treatment: 19631688 INFO @ Sun, 21 Jun 2020 18:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:30:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:30:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:30:56: #2 number of paired peaks: 1766 INFO @ Sun, 21 Jun 2020 18:30:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:30:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:30:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:30:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:30:56: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:30:56: #2 alternative fragment length(s) may be 1,47 bps INFO @ Sun, 21 Jun 2020 18:30:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.20_model.r WARNING @ Sun, 21 Jun 2020 18:30:56: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:30:56: #2 You may need to consider one of the other alternative d(s): 1,47 WARNING @ Sun, 21 Jun 2020 18:30:56: #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 18:30:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:30:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:31:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:31:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:31:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:31:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.05_summits.bed INFO @ Sun, 21 Jun 2020 18:31:05: Done! pass1 - making usageList (717 chroms): 1 millis pass2 - checking and writing primary data (3724 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:31:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:31:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:31:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.10_summits.bed INFO @ Sun, 21 Jun 2020 18:31:21: Done! pass1 - making usageList (592 chroms): 1 millis pass2 - checking and writing primary data (2501 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:31:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:31:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:31:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:31:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055966/SRX2055966.20_summits.bed INFO @ Sun, 21 Jun 2020 18:31:52: Done! pass1 - making usageList (456 chroms): 1 millis pass2 - checking and writing primary data (1574 records, 4 fields): 15 millis CompletedMACS2peakCalling