Job ID = 6457485 SRX = SRX4664643 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:48:51 prefetch.2.10.7: 1) Downloading 'SRR7813070'... 2020-06-21T11:48:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:52:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:52:53 prefetch.2.10.7: 1) 'SRR7813070' was downloaded successfully Read 26009505 spots for SRR7813070/SRR7813070.sra Written 26009505 spots for SRR7813070/SRR7813070.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: 00:07:50 26009505 reads; of these: 26009505 (100.00%) were unpaired; of these: 853379 (3.28%) aligned 0 times 17336382 (66.65%) aligned exactly 1 time 7819744 (30.06%) aligned >1 times 96.72% overall alignment rate Time searching: 00:07:50 Overall time: 00:07:50 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_sort_core] merging from 12 files... [bam_rmdupse_core] 4524846 / 25156126 = 0.1799 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 21:07:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.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 21:07:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:07:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:28: 1000000 INFO @ Sun, 21 Jun 2020 21:07:33: 2000000 INFO @ Sun, 21 Jun 2020 21:07:37: 3000000 INFO @ Sun, 21 Jun 2020 21:07:42: 4000000 INFO @ Sun, 21 Jun 2020 21:07:47: 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 21:07:52: 6000000 INFO @ Sun, 21 Jun 2020 21:07:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.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 21:07:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:07:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:57: 7000000 INFO @ Sun, 21 Jun 2020 21:07:58: 1000000 INFO @ Sun, 21 Jun 2020 21:08:02: 8000000 INFO @ Sun, 21 Jun 2020 21:08:03: 2000000 INFO @ Sun, 21 Jun 2020 21:08:07: 9000000 INFO @ Sun, 21 Jun 2020 21:08:08: 3000000 INFO @ Sun, 21 Jun 2020 21:08:12: 10000000 INFO @ Sun, 21 Jun 2020 21:08:13: 4000000 INFO @ Sun, 21 Jun 2020 21:08:17: 11000000 INFO @ Sun, 21 Jun 2020 21:08:18: 5000000 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 21:08:22: 12000000 INFO @ Sun, 21 Jun 2020 21:08:23: 6000000 INFO @ Sun, 21 Jun 2020 21:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.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 21:08:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:08:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:08:27: 13000000 INFO @ Sun, 21 Jun 2020 21:08:28: 1000000 INFO @ Sun, 21 Jun 2020 21:08:28: 7000000 INFO @ Sun, 21 Jun 2020 21:08:32: 14000000 INFO @ Sun, 21 Jun 2020 21:08:33: 2000000 INFO @ Sun, 21 Jun 2020 21:08:34: 8000000 INFO @ Sun, 21 Jun 2020 21:08:37: 15000000 INFO @ Sun, 21 Jun 2020 21:08:39: 3000000 INFO @ Sun, 21 Jun 2020 21:08:39: 9000000 INFO @ Sun, 21 Jun 2020 21:08:42: 16000000 INFO @ Sun, 21 Jun 2020 21:08:44: 4000000 INFO @ Sun, 21 Jun 2020 21:08:44: 10000000 INFO @ Sun, 21 Jun 2020 21:08:47: 17000000 INFO @ Sun, 21 Jun 2020 21:08:49: 5000000 INFO @ Sun, 21 Jun 2020 21:08:49: 11000000 INFO @ Sun, 21 Jun 2020 21:08:53: 18000000 INFO @ Sun, 21 Jun 2020 21:08:54: 12000000 INFO @ Sun, 21 Jun 2020 21:08:54: 6000000 INFO @ Sun, 21 Jun 2020 21:08:58: 19000000 INFO @ Sun, 21 Jun 2020 21:08:59: 13000000 INFO @ Sun, 21 Jun 2020 21:08:59: 7000000 INFO @ Sun, 21 Jun 2020 21:09:03: 20000000 INFO @ Sun, 21 Jun 2020 21:09:04: 14000000 INFO @ Sun, 21 Jun 2020 21:09:04: 8000000 INFO @ Sun, 21 Jun 2020 21:09:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:09:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:09:06: #1 total tags in treatment: 20631280 INFO @ Sun, 21 Jun 2020 21:09:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:09:06: #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 21:09:07: #1 tags after filtering in treatment: 20631204 INFO @ Sun, 21 Jun 2020 21:09:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:09:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:09:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:09:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:09:08: #2 number of paired peaks: 1259 INFO @ Sun, 21 Jun 2020 21:09:08: start model_add_line... INFO @ Sun, 21 Jun 2020 21:09:08: start X-correlation... INFO @ Sun, 21 Jun 2020 21:09:08: end of X-cor INFO @ Sun, 21 Jun 2020 21:09:08: #2 finished! INFO @ Sun, 21 Jun 2020 21:09:08: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 21:09:08: #2 alternative fragment length(s) may be 2,53 bps INFO @ Sun, 21 Jun 2020 21:09:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.05_model.r WARNING @ Sun, 21 Jun 2020 21:09:08: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:09:08: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Sun, 21 Jun 2020 21:09:08: #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 21:09:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:09:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:09:09: 15000000 INFO @ Sun, 21 Jun 2020 21:09:09: 9000000 INFO @ Sun, 21 Jun 2020 21:09:14: 16000000 INFO @ Sun, 21 Jun 2020 21:09:15: 10000000 INFO @ Sun, 21 Jun 2020 21:09:19: 17000000 INFO @ Sun, 21 Jun 2020 21:09:20: 11000000 INFO @ Sun, 21 Jun 2020 21:09:25: 18000000 INFO @ Sun, 21 Jun 2020 21:09:25: 12000000 INFO @ Sun, 21 Jun 2020 21:09:30: 19000000 INFO @ Sun, 21 Jun 2020 21:09:30: 13000000 INFO @ Sun, 21 Jun 2020 21:09:35: 20000000 INFO @ Sun, 21 Jun 2020 21:09:35: 14000000 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: 20631280 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 21:09:39: #1 tags after filtering in treatment: 20631204 INFO @ Sun, 21 Jun 2020 21:09:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:09:39: #1 finished! INFO @ Sun, 21 Jun 2020 21:09:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:09:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:09:40: 15000000 INFO @ Sun, 21 Jun 2020 21:09:40: #2 number of paired peaks: 1259 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 53 bps INFO @ Sun, 21 Jun 2020 21:09:40: #2 alternative fragment length(s) may be 2,53 bps INFO @ Sun, 21 Jun 2020 21:09:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.10_model.r WARNING @ Sun, 21 Jun 2020 21:09:40: #2 Since the d (53) 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): 2,53 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 21:09:45: 16000000 INFO @ Sun, 21 Jun 2020 21:09:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:09:50: 17000000 INFO @ Sun, 21 Jun 2020 21:09:55: 18000000 INFO @ Sun, 21 Jun 2020 21:10:00: 19000000 INFO @ Sun, 21 Jun 2020 21:10:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:10:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:10:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.05_summits.bed INFO @ Sun, 21 Jun 2020 21:10:04: Done! pass1 - making usageList (601 chroms): 1 millis pass2 - checking and writing primary data (4861 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:10:05: 20000000 INFO @ Sun, 21 Jun 2020 21:10:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:10:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:10:08: #1 total tags in treatment: 20631280 INFO @ Sun, 21 Jun 2020 21:10:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:10:08: #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 21:10:09: #1 tags after filtering in treatment: 20631204 INFO @ Sun, 21 Jun 2020 21:10:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:10:09: #1 finished! INFO @ Sun, 21 Jun 2020 21:10:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:10:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:10:10: #2 number of paired peaks: 1259 INFO @ Sun, 21 Jun 2020 21:10:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:10:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:10:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:10:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:10:10: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 21:10:10: #2 alternative fragment length(s) may be 2,53 bps INFO @ Sun, 21 Jun 2020 21:10:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.20_model.r WARNING @ Sun, 21 Jun 2020 21:10:10: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:10:10: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Sun, 21 Jun 2020 21:10:10: #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 21:10:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:10:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:10:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:10:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:10:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:10:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.10_summits.bed INFO @ Sun, 21 Jun 2020 21:10:37: Done! pass1 - making usageList (516 chroms): 1 millis pass2 - checking and writing primary data (2874 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:10:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:11:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:11:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:11:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664643/SRX4664643.20_summits.bed INFO @ Sun, 21 Jun 2020 21:11:06: Done! pass1 - making usageList (381 chroms): 1 millis pass2 - checking and writing primary data (1157 records, 4 fields): 12 millis CompletedMACS2peakCalling