Job ID = 6455408 SRX = SRX287763 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:57:25 prefetch.2.10.7: 1) Downloading 'SRR869952'... 2020-06-21T09:57:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:01:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:01:01 prefetch.2.10.7: 1) 'SRR869952' was downloaded successfully Read 22382823 spots for SRR869952/SRR869952.sra Written 22382823 spots for SRR869952/SRR869952.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: 00:06:16 22382823 reads; of these: 22382823 (100.00%) were unpaired; of these: 1401489 (6.26%) aligned 0 times 14498660 (64.78%) aligned exactly 1 time 6482674 (28.96%) aligned >1 times 93.74% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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 12 files... [bam_rmdupse_core] 5661640 / 20981334 = 0.2698 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 19:13:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.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 19:13:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:47: 1000000 INFO @ Sun, 21 Jun 2020 19:13:53: 2000000 INFO @ Sun, 21 Jun 2020 19:13:58: 3000000 INFO @ Sun, 21 Jun 2020 19:14:04: 4000000 INFO @ Sun, 21 Jun 2020 19:14:09: 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 19:14:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.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 19:14:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:15: 6000000 INFO @ Sun, 21 Jun 2020 19:14:18: 1000000 INFO @ Sun, 21 Jun 2020 19:14:22: 7000000 INFO @ Sun, 21 Jun 2020 19:14:24: 2000000 INFO @ Sun, 21 Jun 2020 19:14:28: 8000000 INFO @ Sun, 21 Jun 2020 19:14:30: 3000000 INFO @ Sun, 21 Jun 2020 19:14:34: 9000000 INFO @ Sun, 21 Jun 2020 19:14:37: 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 19:14:40: 10000000 INFO @ Sun, 21 Jun 2020 19:14:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.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 19:14:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:43: 5000000 INFO @ Sun, 21 Jun 2020 19:14:47: 11000000 INFO @ Sun, 21 Jun 2020 19:14:48: 1000000 INFO @ Sun, 21 Jun 2020 19:14:49: 6000000 INFO @ Sun, 21 Jun 2020 19:14:53: 12000000 INFO @ Sun, 21 Jun 2020 19:14:54: 2000000 INFO @ Sun, 21 Jun 2020 19:14:56: 7000000 INFO @ Sun, 21 Jun 2020 19:15:00: 13000000 INFO @ Sun, 21 Jun 2020 19:15:01: 3000000 INFO @ Sun, 21 Jun 2020 19:15:02: 8000000 INFO @ Sun, 21 Jun 2020 19:15:06: 14000000 INFO @ Sun, 21 Jun 2020 19:15:07: 4000000 INFO @ Sun, 21 Jun 2020 19:15:09: 9000000 INFO @ Sun, 21 Jun 2020 19:15:13: 15000000 INFO @ Sun, 21 Jun 2020 19:15:14: 5000000 INFO @ Sun, 21 Jun 2020 19:15:15: 10000000 INFO @ Sun, 21 Jun 2020 19:15:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:15: #1 total tags in treatment: 15319694 INFO @ Sun, 21 Jun 2020 19:15:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:15: #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 19:15:16: #1 tags after filtering in treatment: 15319694 INFO @ Sun, 21 Jun 2020 19:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:17: #2 number of paired peaks: 815 WARNING @ Sun, 21 Jun 2020 19:15:17: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:17: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:15:17: #2 alternative fragment length(s) may be 2,35 bps INFO @ Sun, 21 Jun 2020 19:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.05_model.r WARNING @ Sun, 21 Jun 2020 19:15:17: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:17: #2 You may need to consider one of the other alternative d(s): 2,35 WARNING @ Sun, 21 Jun 2020 19:15:17: #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 19:15:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:20: 6000000 INFO @ Sun, 21 Jun 2020 19:15:22: 11000000 INFO @ Sun, 21 Jun 2020 19:15:27: 7000000 INFO @ Sun, 21 Jun 2020 19:15:28: 12000000 INFO @ Sun, 21 Jun 2020 19:15:33: 8000000 INFO @ Sun, 21 Jun 2020 19:15:35: 13000000 INFO @ Sun, 21 Jun 2020 19:15:39: 9000000 INFO @ Sun, 21 Jun 2020 19:15:42: 14000000 INFO @ Sun, 21 Jun 2020 19:15:46: 10000000 INFO @ Sun, 21 Jun 2020 19:15:48: 15000000 INFO @ Sun, 21 Jun 2020 19:15:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:51: #1 total tags in treatment: 15319694 INFO @ Sun, 21 Jun 2020 19:15:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:51: #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 19:15:51: #1 tags after filtering in treatment: 15319694 INFO @ Sun, 21 Jun 2020 19:15:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:52: #2 number of paired peaks: 815 WARNING @ Sun, 21 Jun 2020 19:15:52: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:52: 11000000 INFO @ Sun, 21 Jun 2020 19:15:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:52: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:15:52: #2 alternative fragment length(s) may be 2,35 bps INFO @ Sun, 21 Jun 2020 19:15:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.10_model.r WARNING @ Sun, 21 Jun 2020 19:15:52: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:52: #2 You may need to consider one of the other alternative d(s): 2,35 WARNING @ Sun, 21 Jun 2020 19:15:52: #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 19:15:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:52: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:15:59: 12000000 INFO @ Sun, 21 Jun 2020 19:16:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.05_summits.bed INFO @ Sun, 21 Jun 2020 19:16:04: Done! pass1 - making usageList (670 chroms): 1 millis pass2 - checking and writing primary data (2528 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:05: 13000000 INFO @ Sun, 21 Jun 2020 19:16:11: 14000000 INFO @ Sun, 21 Jun 2020 19:16:17: 15000000 INFO @ Sun, 21 Jun 2020 19:16:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:19: #1 total tags in treatment: 15319694 INFO @ Sun, 21 Jun 2020 19:16:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:19: #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 19:16:20: #1 tags after filtering in treatment: 15319694 INFO @ Sun, 21 Jun 2020 19:16:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:21: #2 number of paired peaks: 815 WARNING @ Sun, 21 Jun 2020 19:16:21: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:21: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:16:21: #2 alternative fragment length(s) may be 2,35 bps INFO @ Sun, 21 Jun 2020 19:16:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.20_model.r WARNING @ Sun, 21 Jun 2020 19:16:21: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:16:21: #2 You may need to consider one of the other alternative d(s): 2,35 WARNING @ Sun, 21 Jun 2020 19:16:21: #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 19:16:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.10_summits.bed INFO @ Sun, 21 Jun 2020 19:16:40: Done! pass1 - making usageList (530 chroms): 1 millis pass2 - checking and writing primary data (2109 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287763/SRX287763.20_summits.bed INFO @ Sun, 21 Jun 2020 19:17:10: Done! pass1 - making usageList (388 chroms): 1 millis pass2 - checking and writing primary data (1032 records, 4 fields): 13 millis CompletedMACS2peakCalling