Job ID = 6453174 SRX = SRX1050603 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:33:09 prefetch.2.10.7: 1) Downloading 'SRR2053191'... 2020-06-21T08:33:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:36:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:36:06 prefetch.2.10.7: 1) 'SRR2053191' was downloaded successfully Read 17724933 spots for SRR2053191/SRR2053191.sra Written 17724933 spots for SRR2053191/SRR2053191.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: 00:05:26 17724933 reads; of these: 17724933 (100.00%) were unpaired; of these: 2005357 (11.31%) aligned 0 times 11600401 (65.45%) aligned exactly 1 time 4119175 (23.24%) aligned >1 times 88.69% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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] 2427959 / 15719576 = 0.1545 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 17:48:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.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 17:48:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:42: 1000000 INFO @ Sun, 21 Jun 2020 17:48:51: 2000000 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 17:49:00: 3000000 INFO @ Sun, 21 Jun 2020 17:49:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.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 17:49:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:10: 4000000 INFO @ Sun, 21 Jun 2020 17:49:11: 1000000 INFO @ Sun, 21 Jun 2020 17:49:19: 5000000 INFO @ Sun, 21 Jun 2020 17:49:20: 2000000 INFO @ Sun, 21 Jun 2020 17:49:29: 3000000 INFO @ Sun, 21 Jun 2020 17:49:29: 6000000 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 17:49:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.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 17:49:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:38: 7000000 INFO @ Sun, 21 Jun 2020 17:49:39: 4000000 INFO @ Sun, 21 Jun 2020 17:49:42: 1000000 INFO @ Sun, 21 Jun 2020 17:49:48: 8000000 INFO @ Sun, 21 Jun 2020 17:49:48: 5000000 INFO @ Sun, 21 Jun 2020 17:49:52: 2000000 INFO @ Sun, 21 Jun 2020 17:49:57: 9000000 INFO @ Sun, 21 Jun 2020 17:49:58: 6000000 INFO @ Sun, 21 Jun 2020 17:50:02: 3000000 INFO @ Sun, 21 Jun 2020 17:50:06: 10000000 INFO @ Sun, 21 Jun 2020 17:50:09: 7000000 INFO @ Sun, 21 Jun 2020 17:50:12: 4000000 INFO @ Sun, 21 Jun 2020 17:50:15: 11000000 INFO @ Sun, 21 Jun 2020 17:50:19: 8000000 INFO @ Sun, 21 Jun 2020 17:50:22: 5000000 INFO @ Sun, 21 Jun 2020 17:50:23: 12000000 INFO @ Sun, 21 Jun 2020 17:50:29: 9000000 INFO @ Sun, 21 Jun 2020 17:50:32: 13000000 INFO @ Sun, 21 Jun 2020 17:50:32: 6000000 INFO @ Sun, 21 Jun 2020 17:50:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:50:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:50:34: #1 total tags in treatment: 13291617 INFO @ Sun, 21 Jun 2020 17:50:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:34: #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 17:50:35: #1 tags after filtering in treatment: 13291617 INFO @ Sun, 21 Jun 2020 17:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:36: #2 number of paired peaks: 271 WARNING @ Sun, 21 Jun 2020 17:50:36: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Sun, 21 Jun 2020 17:50:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:36: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 17:50:36: #2 alternative fragment length(s) may be 3,42,562 bps INFO @ Sun, 21 Jun 2020 17:50:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.05_model.r WARNING @ Sun, 21 Jun 2020 17:50:36: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:50:36: #2 You may need to consider one of the other alternative d(s): 3,42,562 WARNING @ Sun, 21 Jun 2020 17:50:36: #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 17:50:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:50:39: 10000000 INFO @ Sun, 21 Jun 2020 17:50:43: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:50:50: 11000000 INFO @ Sun, 21 Jun 2020 17:50:53: 8000000 INFO @ Sun, 21 Jun 2020 17:51:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:51:01: 12000000 INFO @ Sun, 21 Jun 2020 17:51:04: 9000000 INFO @ Sun, 21 Jun 2020 17:51:12: 13000000 INFO @ Sun, 21 Jun 2020 17:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.05_summits.bed INFO @ Sun, 21 Jun 2020 17:51:13: Done! pass1 - making usageList (490 chroms): 1 millis pass2 - checking and writing primary data (1725 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:51:14: 10000000 INFO @ Sun, 21 Jun 2020 17:51:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:51:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:51:15: #1 total tags in treatment: 13291617 INFO @ Sun, 21 Jun 2020 17:51:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:51:15: #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 17:51:16: #1 tags after filtering in treatment: 13291617 INFO @ Sun, 21 Jun 2020 17:51:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:51:16: #1 finished! INFO @ Sun, 21 Jun 2020 17:51:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:51:17: #2 number of paired peaks: 271 WARNING @ Sun, 21 Jun 2020 17:51:17: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Sun, 21 Jun 2020 17:51:17: start model_add_line... INFO @ Sun, 21 Jun 2020 17:51:17: start X-correlation... INFO @ Sun, 21 Jun 2020 17:51:17: end of X-cor INFO @ Sun, 21 Jun 2020 17:51:17: #2 finished! INFO @ Sun, 21 Jun 2020 17:51:17: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 17:51:17: #2 alternative fragment length(s) may be 3,42,562 bps INFO @ Sun, 21 Jun 2020 17:51:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.10_model.r WARNING @ Sun, 21 Jun 2020 17:51:17: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:51:17: #2 You may need to consider one of the other alternative d(s): 3,42,562 WARNING @ Sun, 21 Jun 2020 17:51:17: #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 17:51:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:51:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:51:25: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:51:35: 12000000 INFO @ Sun, 21 Jun 2020 17:51:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:51:46: 13000000 INFO @ Sun, 21 Jun 2020 17:51:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:51:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:51:49: #1 total tags in treatment: 13291617 INFO @ Sun, 21 Jun 2020 17:51:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:51:49: #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 17:51:50: #1 tags after filtering in treatment: 13291617 INFO @ Sun, 21 Jun 2020 17:51:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:51:50: #1 finished! INFO @ Sun, 21 Jun 2020 17:51:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:51:51: #2 number of paired peaks: 271 WARNING @ Sun, 21 Jun 2020 17:51:51: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Sun, 21 Jun 2020 17:51:51: start model_add_line... INFO @ Sun, 21 Jun 2020 17:51:51: start X-correlation... INFO @ Sun, 21 Jun 2020 17:51:51: end of X-cor INFO @ Sun, 21 Jun 2020 17:51:51: #2 finished! INFO @ Sun, 21 Jun 2020 17:51:51: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 17:51:51: #2 alternative fragment length(s) may be 3,42,562 bps INFO @ Sun, 21 Jun 2020 17:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.20_model.r WARNING @ Sun, 21 Jun 2020 17:51:51: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:51:51: #2 You may need to consider one of the other alternative d(s): 3,42,562 WARNING @ Sun, 21 Jun 2020 17:51:51: #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 17:51:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:51:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:51:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:51:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.10_summits.bed INFO @ Sun, 21 Jun 2020 17:51:53: Done! pass1 - making usageList (315 chroms): 2 millis pass2 - checking and writing primary data (728 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:52:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:52:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1050603/SRX1050603.20_summits.bed INFO @ Sun, 21 Jun 2020 17:52:27: Done! pass1 - making usageList (132 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 9 millis CompletedMACS2peakCalling