Job ID = 6454481 SRX = SRX2165268 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:25:59 prefetch.2.10.7: 1) Downloading 'SRR4244765'... 2020-06-21T09:25:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:29:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:29:51 prefetch.2.10.7: 'SRR4244765' is valid 2020-06-21T09:29:51 prefetch.2.10.7: 1) 'SRR4244765' was downloaded successfully Read 11516541 spots for SRR4244765/SRR4244765.sra Written 11516541 spots for SRR4244765/SRR4244765.sra 2020-06-21T09:30:35 prefetch.2.10.7: 1) Downloading 'SRR4244766'... 2020-06-21T09:30:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:35:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:35:04 prefetch.2.10.7: 1) 'SRR4244766' was downloaded successfully Read 14754328 spots for SRR4244766/SRR4244766.sra Written 14754328 spots for SRR4244766/SRR4244766.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: 00:08:39 26270869 reads; of these: 26270869 (100.00%) were unpaired; of these: 6020462 (22.92%) aligned 0 times 14427074 (54.92%) aligned exactly 1 time 5823333 (22.17%) aligned >1 times 77.08% overall alignment rate Time searching: 00:08:39 Overall time: 00:08:39 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] 8215908 / 20250407 = 0.4057 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 18:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.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 18:50:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:15: 1000000 INFO @ Sun, 21 Jun 2020 18:50:22: 2000000 INFO @ Sun, 21 Jun 2020 18:50:29: 3000000 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 18:50:37: 4000000 INFO @ Sun, 21 Jun 2020 18:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.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 18:50:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:44: 5000000 INFO @ Sun, 21 Jun 2020 18:50:46: 1000000 INFO @ Sun, 21 Jun 2020 18:50:52: 6000000 INFO @ Sun, 21 Jun 2020 18:50:54: 2000000 INFO @ Sun, 21 Jun 2020 18:51:00: 7000000 INFO @ Sun, 21 Jun 2020 18:51:01: 3000000 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 18:51:07: 8000000 INFO @ Sun, 21 Jun 2020 18:51:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.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 18:51:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:09: 4000000 INFO @ Sun, 21 Jun 2020 18:51:15: 9000000 INFO @ Sun, 21 Jun 2020 18:51:15: 1000000 INFO @ Sun, 21 Jun 2020 18:51:17: 5000000 INFO @ Sun, 21 Jun 2020 18:51:23: 2000000 INFO @ Sun, 21 Jun 2020 18:51:23: 10000000 INFO @ Sun, 21 Jun 2020 18:51:25: 6000000 INFO @ Sun, 21 Jun 2020 18:51:31: 3000000 INFO @ Sun, 21 Jun 2020 18:51:31: 11000000 INFO @ Sun, 21 Jun 2020 18:51:33: 7000000 INFO @ Sun, 21 Jun 2020 18:51:38: 4000000 INFO @ Sun, 21 Jun 2020 18:51:39: 12000000 INFO @ Sun, 21 Jun 2020 18:51:39: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:51:39: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:51:39: #1 total tags in treatment: 12034499 INFO @ Sun, 21 Jun 2020 18:51:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:39: #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 18:51:39: #1 tags after filtering in treatment: 12034489 INFO @ Sun, 21 Jun 2020 18:51:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:40: #2 number of paired peaks: 878 WARNING @ Sun, 21 Jun 2020 18:51:40: Fewer paired peaks (878) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 878 pairs to build model! INFO @ Sun, 21 Jun 2020 18:51:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:40: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 18:51:40: #2 alternative fragment length(s) may be 3,61 bps INFO @ Sun, 21 Jun 2020 18:51:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.05_model.r WARNING @ Sun, 21 Jun 2020 18:51:40: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:40: #2 You may need to consider one of the other alternative d(s): 3,61 WARNING @ Sun, 21 Jun 2020 18:51:40: #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 18:51:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:41: 8000000 INFO @ Sun, 21 Jun 2020 18:51:46: 5000000 INFO @ Sun, 21 Jun 2020 18:51:48: 9000000 INFO @ Sun, 21 Jun 2020 18:51:53: 6000000 INFO @ Sun, 21 Jun 2020 18:51:56: 10000000 INFO @ Sun, 21 Jun 2020 18:52:01: 7000000 INFO @ Sun, 21 Jun 2020 18:52:04: 11000000 INFO @ Sun, 21 Jun 2020 18:52:05: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:52:08: 8000000 INFO @ Sun, 21 Jun 2020 18:52:12: 12000000 INFO @ Sun, 21 Jun 2020 18:52:12: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:52:12: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:52:12: #1 total tags in treatment: 12034499 INFO @ Sun, 21 Jun 2020 18:52:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:12: #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 18:52:12: #1 tags after filtering in treatment: 12034489 INFO @ Sun, 21 Jun 2020 18:52:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:13: #2 number of paired peaks: 878 WARNING @ Sun, 21 Jun 2020 18:52:13: Fewer paired peaks (878) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 878 pairs to build model! INFO @ Sun, 21 Jun 2020 18:52:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:13: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 18:52:13: #2 alternative fragment length(s) may be 3,61 bps INFO @ Sun, 21 Jun 2020 18:52:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.10_model.r WARNING @ Sun, 21 Jun 2020 18:52:13: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:13: #2 You may need to consider one of the other alternative d(s): 3,61 WARNING @ Sun, 21 Jun 2020 18:52:13: #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 18:52:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:16: 9000000 INFO @ Sun, 21 Jun 2020 18:52:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.05_summits.bed INFO @ Sun, 21 Jun 2020 18:52:17: Done! pass1 - making usageList (723 chroms): 1 millis pass2 - checking and writing primary data (2602 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:52:23: 10000000 INFO @ Sun, 21 Jun 2020 18:52:30: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:52:37: 12000000 INFO @ Sun, 21 Jun 2020 18:52:37: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:52:37: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:52:37: #1 total tags in treatment: 12034499 INFO @ Sun, 21 Jun 2020 18:52:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:37: #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 18:52:38: #1 tags after filtering in treatment: 12034489 INFO @ Sun, 21 Jun 2020 18:52:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:39: #2 number of paired peaks: 878 WARNING @ Sun, 21 Jun 2020 18:52:39: Fewer paired peaks (878) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 878 pairs to build model! INFO @ Sun, 21 Jun 2020 18:52:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:39: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 18:52:39: #2 alternative fragment length(s) may be 3,61 bps INFO @ Sun, 21 Jun 2020 18:52:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.20_model.r WARNING @ Sun, 21 Jun 2020 18:52:39: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:39: #2 You may need to consider one of the other alternative d(s): 3,61 WARNING @ Sun, 21 Jun 2020 18:52:39: #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 18:52:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.10_summits.bed INFO @ Sun, 21 Jun 2020 18:52:50: Done! pass1 - making usageList (597 chroms): 1 millis pass2 - checking and writing primary data (1871 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:53:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165268/SRX2165268.20_summits.bed INFO @ Sun, 21 Jun 2020 18:53:14: Done! pass1 - making usageList (433 chroms): 1 millis pass2 - checking and writing primary data (1198 records, 4 fields): 12 millis CompletedMACS2peakCalling