Job ID = 6457866 SRX = SRX4823782 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:57:51 prefetch.2.10.7: 1) Downloading 'SRR7992740'... 2020-06-21T11:57:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:02:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:02:13 prefetch.2.10.7: 1) 'SRR7992740' was downloaded successfully 2020-06-21T12:02:13 prefetch.2.10.7: 'SRR7992740' has 0 unresolved dependencies Read 49157846 spots for SRR7992740/SRR7992740.sra Written 49157846 spots for SRR7992740/SRR7992740.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: 00:13:16 49157846 reads; of these: 49157846 (100.00%) were unpaired; of these: 9712416 (19.76%) aligned 0 times 26914254 (54.75%) aligned exactly 1 time 12531176 (25.49%) aligned >1 times 80.24% overall alignment rate Time searching: 00:13:16 Overall time: 00:13:16 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 20 files... [bam_rmdupse_core] 29018437 / 39445430 = 0.7357 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 21:23:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.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 21:23:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:23:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:23:38: 1000000 INFO @ Sun, 21 Jun 2020 21:23:45: 2000000 INFO @ Sun, 21 Jun 2020 21:23:52: 3000000 INFO @ Sun, 21 Jun 2020 21:23:59: 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 21:24:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.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 21:24:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:24:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:24:06: 5000000 INFO @ Sun, 21 Jun 2020 21:24:08: 1000000 INFO @ Sun, 21 Jun 2020 21:24:13: 6000000 INFO @ Sun, 21 Jun 2020 21:24:15: 2000000 INFO @ Sun, 21 Jun 2020 21:24:20: 7000000 INFO @ Sun, 21 Jun 2020 21:24:22: 3000000 INFO @ Sun, 21 Jun 2020 21:24:28: 8000000 INFO @ Sun, 21 Jun 2020 21:24:28: 4000000 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 21:24:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.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 21:24:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:24:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:24:35: 5000000 INFO @ Sun, 21 Jun 2020 21:24:36: 9000000 INFO @ Sun, 21 Jun 2020 21:24:38: 1000000 INFO @ Sun, 21 Jun 2020 21:24:43: 6000000 INFO @ Sun, 21 Jun 2020 21:24:43: 10000000 INFO @ Sun, 21 Jun 2020 21:24:46: 2000000 INFO @ Sun, 21 Jun 2020 21:24:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:24:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:24:46: #1 total tags in treatment: 10426993 INFO @ Sun, 21 Jun 2020 21:24:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:24:46: #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 21:24:47: #1 tags after filtering in treatment: 10426940 INFO @ Sun, 21 Jun 2020 21:24:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:24:47: #1 finished! INFO @ Sun, 21 Jun 2020 21:24:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:24:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:24:47: #2 number of paired peaks: 2205 INFO @ Sun, 21 Jun 2020 21:24:47: start model_add_line... INFO @ Sun, 21 Jun 2020 21:24:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:24:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:24:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:24:48: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:24:48: #2 alternative fragment length(s) may be 2,43,560 bps INFO @ Sun, 21 Jun 2020 21:24:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.05_model.r WARNING @ Sun, 21 Jun 2020 21:24:48: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:24:48: #2 You may need to consider one of the other alternative d(s): 2,43,560 WARNING @ Sun, 21 Jun 2020 21:24:48: #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 21:24:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:24:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:24:49: 7000000 INFO @ Sun, 21 Jun 2020 21:24:52: 3000000 INFO @ Sun, 21 Jun 2020 21:24:56: 8000000 INFO @ Sun, 21 Jun 2020 21:24:59: 4000000 INFO @ Sun, 21 Jun 2020 21:25:03: 9000000 INFO @ Sun, 21 Jun 2020 21:25:05: 5000000 INFO @ Sun, 21 Jun 2020 21:25:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:25:09: 10000000 INFO @ Sun, 21 Jun 2020 21:25:12: 6000000 INFO @ Sun, 21 Jun 2020 21:25:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:25:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:25:12: #1 total tags in treatment: 10426993 INFO @ Sun, 21 Jun 2020 21:25:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:12: #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 21:25:12: #1 tags after filtering in treatment: 10426940 INFO @ Sun, 21 Jun 2020 21:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:12: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:13: #2 number of paired peaks: 2205 INFO @ Sun, 21 Jun 2020 21:25:13: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:13: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:25:13: #2 alternative fragment length(s) may be 2,43,560 bps INFO @ Sun, 21 Jun 2020 21:25:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.10_model.r WARNING @ Sun, 21 Jun 2020 21:25:13: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:25:13: #2 You may need to consider one of the other alternative d(s): 2,43,560 WARNING @ Sun, 21 Jun 2020 21:25:13: #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 21:25:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:25:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:25:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.05_summits.bed INFO @ Sun, 21 Jun 2020 21:25:17: Done! INFO @ Sun, 21 Jun 2020 21:25:18: 7000000 pass1 - making usageList (854 chroms): 2 millis pass2 - checking and writing primary data (3977 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:25:24: 8000000 INFO @ Sun, 21 Jun 2020 21:25:30: 9000000 INFO @ Sun, 21 Jun 2020 21:25:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:25:35: 10000000 INFO @ Sun, 21 Jun 2020 21:25:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:25:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:25:38: #1 total tags in treatment: 10426993 INFO @ Sun, 21 Jun 2020 21:25:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:38: #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 21:25:38: #1 tags after filtering in treatment: 10426940 INFO @ Sun, 21 Jun 2020 21:25:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:38: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:39: #2 number of paired peaks: 2205 INFO @ Sun, 21 Jun 2020 21:25:39: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:39: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:39: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:39: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:39: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:25:39: #2 alternative fragment length(s) may be 2,43,560 bps INFO @ Sun, 21 Jun 2020 21:25:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.20_model.r WARNING @ Sun, 21 Jun 2020 21:25:39: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:25:39: #2 You may need to consider one of the other alternative d(s): 2,43,560 WARNING @ Sun, 21 Jun 2020 21:25:39: #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 21:25:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:25:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:25:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:25:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.10_summits.bed INFO @ Sun, 21 Jun 2020 21:25:43: Done! pass1 - making usageList (701 chroms): 2 millis pass2 - checking and writing primary data (2725 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:25:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:26:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:26:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:26:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823782/SRX4823782.20_summits.bed INFO @ Sun, 21 Jun 2020 21:26:09: Done! pass1 - making usageList (564 chroms): 1 millis pass2 - checking and writing primary data (2022 records, 4 fields): 17 millis CompletedMACS2peakCalling