Job ID = 6455421 SRX = SRX287775 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:13:51 prefetch.2.10.7: 1) Downloading 'SRR869964'... 2020-06-21T10:13:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:16:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:16:21 prefetch.2.10.7: 'SRR869964' is valid 2020-06-21T10:16:21 prefetch.2.10.7: 1) 'SRR869964' was downloaded successfully Read 13922297 spots for SRR869964/SRR869964.sra Written 13922297 spots for SRR869964/SRR869964.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: 00:04:16 13922297 reads; of these: 13922297 (100.00%) were unpaired; of these: 878486 (6.31%) aligned 0 times 9210050 (66.15%) aligned exactly 1 time 3833761 (27.54%) aligned >1 times 93.69% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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 8 files... [bam_rmdupse_core] 2436423 / 13043811 = 0.1868 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 19:24:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.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 19:24:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:02: 1000000 INFO @ Sun, 21 Jun 2020 19:25:09: 2000000 INFO @ Sun, 21 Jun 2020 19:25:15: 3000000 INFO @ Sun, 21 Jun 2020 19:25:21: 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 19:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.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 19:25:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:27: 5000000 INFO @ Sun, 21 Jun 2020 19:25:32: 1000000 INFO @ Sun, 21 Jun 2020 19:25:34: 6000000 INFO @ Sun, 21 Jun 2020 19:25:39: 2000000 INFO @ Sun, 21 Jun 2020 19:25:40: 7000000 INFO @ Sun, 21 Jun 2020 19:25:45: 3000000 INFO @ Sun, 21 Jun 2020 19:25:46: 8000000 INFO @ Sun, 21 Jun 2020 19:25:52: 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 19:25:53: 9000000 INFO @ Sun, 21 Jun 2020 19:25:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.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 19:25:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:58: 5000000 INFO @ Sun, 21 Jun 2020 19:26:01: 10000000 INFO @ Sun, 21 Jun 2020 19:26:02: 1000000 INFO @ Sun, 21 Jun 2020 19:26:05: 6000000 INFO @ Sun, 21 Jun 2020 19:26:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:05: #1 total tags in treatment: 10607388 INFO @ Sun, 21 Jun 2020 19:26:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:05: #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 19:26:06: #1 tags after filtering in treatment: 10607386 INFO @ Sun, 21 Jun 2020 19:26:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:06: #2 number of paired peaks: 521 WARNING @ Sun, 21 Jun 2020 19:26:06: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Sun, 21 Jun 2020 19:26:06: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:06: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:06: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:06: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:06: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:26:06: #2 alternative fragment length(s) may be 4,54,595,597 bps INFO @ Sun, 21 Jun 2020 19:26:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.05_model.r WARNING @ Sun, 21 Jun 2020 19:26:06: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:26:06: #2 You may need to consider one of the other alternative d(s): 4,54,595,597 WARNING @ Sun, 21 Jun 2020 19:26:06: #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 19:26:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:09: 2000000 INFO @ Sun, 21 Jun 2020 19:26:11: 7000000 INFO @ Sun, 21 Jun 2020 19:26:16: 3000000 INFO @ Sun, 21 Jun 2020 19:26:18: 8000000 INFO @ Sun, 21 Jun 2020 19:26:23: 4000000 INFO @ Sun, 21 Jun 2020 19:26:24: 9000000 INFO @ Sun, 21 Jun 2020 19:26:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:29: 5000000 INFO @ Sun, 21 Jun 2020 19:26:31: 10000000 INFO @ Sun, 21 Jun 2020 19:26:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:35: #1 total tags in treatment: 10607388 INFO @ Sun, 21 Jun 2020 19:26:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:35: #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 19:26:35: #1 tags after filtering in treatment: 10607386 INFO @ Sun, 21 Jun 2020 19:26:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:36: #2 number of paired peaks: 521 WARNING @ Sun, 21 Jun 2020 19:26:36: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Sun, 21 Jun 2020 19:26:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:36: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:26:36: #2 alternative fragment length(s) may be 4,54,595,597 bps INFO @ Sun, 21 Jun 2020 19:26:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.10_model.r WARNING @ Sun, 21 Jun 2020 19:26:36: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:26:36: #2 You may need to consider one of the other alternative d(s): 4,54,595,597 WARNING @ Sun, 21 Jun 2020 19:26:36: #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 19:26:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:36: 6000000 INFO @ Sun, 21 Jun 2020 19:26:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.05_summits.bed INFO @ Sun, 21 Jun 2020 19:26:39: Done! pass1 - making usageList (643 chroms): 1 millis pass2 - checking and writing primary data (2306 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:26:43: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:26:49: 8000000 INFO @ Sun, 21 Jun 2020 19:26:56: 9000000 INFO @ Sun, 21 Jun 2020 19:26:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:27:03: 10000000 INFO @ Sun, 21 Jun 2020 19:27:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:07: #1 total tags in treatment: 10607388 INFO @ Sun, 21 Jun 2020 19:27:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:07: #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 19:27:07: #1 tags after filtering in treatment: 10607386 INFO @ Sun, 21 Jun 2020 19:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.10_peaks.xls BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.10_summits.bed INFO @ Sun, 21 Jun 2020 19:27:08: Done! INFO @ Sun, 21 Jun 2020 19:27:08: #2 number of paired peaks: 521 WARNING @ Sun, 21 Jun 2020 19:27:08: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Sun, 21 Jun 2020 19:27:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:08: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:27:08: #2 alternative fragment length(s) may be 4,54,595,597 bps INFO @ Sun, 21 Jun 2020 19:27:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.20_model.r WARNING @ Sun, 21 Jun 2020 19:27:08: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:27:08: #2 You may need to consider one of the other alternative d(s): 4,54,595,597 WARNING @ Sun, 21 Jun 2020 19:27:08: #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 19:27:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:08: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (515 chroms): 2 millis pass2 - checking and writing primary data (1617 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:27:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:27:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287775/SRX287775.20_summits.bed INFO @ Sun, 21 Jun 2020 19:27:40: Done! pass1 - making usageList (249 chroms): 1 millis pass2 - checking and writing primary data (456 records, 4 fields): 9 millis CompletedMACS2peakCalling