Job ID = 6509241 SRX = SRX760382 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:32:37 prefetch.2.10.7: 1) Downloading 'SRR1653483'... 2020-06-26T15:32:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:34:42 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:34:42 prefetch.2.10.7: 1) 'SRR1653483' was downloaded successfully Read 22379909 spots for SRR1653483/SRR1653483.sra Written 22379909 spots for SRR1653483/SRR1653483.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: 00:06:11 22379909 reads; of these: 22379909 (100.00%) were unpaired; of these: 4145987 (18.53%) aligned 0 times 9680327 (43.25%) aligned exactly 1 time 8553595 (38.22%) aligned >1 times 81.47% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 6988754 / 18233922 = 0.3833 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 @ Sat, 27 Jun 2020 00:46:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.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 @ Sat, 27 Jun 2020 00:46:15: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:46:15: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:46:22: 1000000 INFO @ Sat, 27 Jun 2020 00:46:28: 2000000 INFO @ Sat, 27 Jun 2020 00:46:34: 3000000 INFO @ Sat, 27 Jun 2020 00:46:40: 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 @ Sat, 27 Jun 2020 00:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.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 @ Sat, 27 Jun 2020 00:46:45: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:46:45: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:46:46: 5000000 INFO @ Sat, 27 Jun 2020 00:46:52: 1000000 INFO @ Sat, 27 Jun 2020 00:46:53: 6000000 INFO @ Sat, 27 Jun 2020 00:46:59: 7000000 INFO @ Sat, 27 Jun 2020 00:47:00: 2000000 INFO @ Sat, 27 Jun 2020 00:47:05: 8000000 INFO @ Sat, 27 Jun 2020 00:47:07: 3000000 INFO @ Sat, 27 Jun 2020 00:47:12: 9000000 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 @ Sat, 27 Jun 2020 00:47:15: 4000000 INFO @ Sat, 27 Jun 2020 00:47:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.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 @ Sat, 27 Jun 2020 00:47:15: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:47:15: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:47:19: 10000000 INFO @ Sat, 27 Jun 2020 00:47:22: 1000000 INFO @ Sat, 27 Jun 2020 00:47:22: 5000000 INFO @ Sat, 27 Jun 2020 00:47:25: 11000000 INFO @ Sat, 27 Jun 2020 00:47:27: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:47:27: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:47:27: #1 total tags in treatment: 11245168 INFO @ Sat, 27 Jun 2020 00:47:27: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:47:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:47:28: #1 tags after filtering in treatment: 11245166 INFO @ Sat, 27 Jun 2020 00:47:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:47:28: #1 finished! INFO @ Sat, 27 Jun 2020 00:47:28: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:47:28: #2 number of paired peaks: 726 WARNING @ Sat, 27 Jun 2020 00:47:28: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Sat, 27 Jun 2020 00:47:28: start model_add_line... INFO @ Sat, 27 Jun 2020 00:47:28: start X-correlation... INFO @ Sat, 27 Jun 2020 00:47:28: end of X-cor INFO @ Sat, 27 Jun 2020 00:47:28: #2 finished! INFO @ Sat, 27 Jun 2020 00:47:28: #2 predicted fragment length is 46 bps INFO @ Sat, 27 Jun 2020 00:47:28: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sat, 27 Jun 2020 00:47:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.05_model.r WARNING @ Sat, 27 Jun 2020 00:47:28: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:47:28: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sat, 27 Jun 2020 00:47:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:47:28: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:47:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:47:29: 2000000 INFO @ Sat, 27 Jun 2020 00:47:29: 6000000 INFO @ Sat, 27 Jun 2020 00:47:37: 7000000 INFO @ Sat, 27 Jun 2020 00:47:37: 3000000 INFO @ Sat, 27 Jun 2020 00:47:44: 8000000 INFO @ Sat, 27 Jun 2020 00:47:44: 4000000 INFO @ Sat, 27 Jun 2020 00:47:51: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:47:52: 9000000 INFO @ Sat, 27 Jun 2020 00:47:52: 5000000 INFO @ Sat, 27 Jun 2020 00:47:59: 10000000 INFO @ Sat, 27 Jun 2020 00:47:59: 6000000 INFO @ Sat, 27 Jun 2020 00:48:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:48:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:48:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.05_summits.bed INFO @ Sat, 27 Jun 2020 00:48:02: Done! pass1 - making usageList (617 chroms): 2 millis pass2 - checking and writing primary data (3844 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:48:06: 7000000 INFO @ Sat, 27 Jun 2020 00:48:06: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:48:08: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:48:08: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:48:08: #1 total tags in treatment: 11245168 INFO @ Sat, 27 Jun 2020 00:48:08: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:48:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:48:09: #1 tags after filtering in treatment: 11245166 INFO @ Sat, 27 Jun 2020 00:48:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:48:09: #1 finished! INFO @ Sat, 27 Jun 2020 00:48:09: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:48:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:48:09: #2 number of paired peaks: 726 WARNING @ Sat, 27 Jun 2020 00:48:09: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Sat, 27 Jun 2020 00:48:09: start model_add_line... INFO @ Sat, 27 Jun 2020 00:48:09: start X-correlation... INFO @ Sat, 27 Jun 2020 00:48:09: end of X-cor INFO @ Sat, 27 Jun 2020 00:48:09: #2 finished! INFO @ Sat, 27 Jun 2020 00:48:09: #2 predicted fragment length is 46 bps INFO @ Sat, 27 Jun 2020 00:48:09: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sat, 27 Jun 2020 00:48:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.10_model.r WARNING @ Sat, 27 Jun 2020 00:48:10: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:48:10: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sat, 27 Jun 2020 00:48:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:48:10: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:48:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:48:13: 8000000 INFO @ Sat, 27 Jun 2020 00:48:20: 9000000 INFO @ Sat, 27 Jun 2020 00:48:27: 10000000 INFO @ Sat, 27 Jun 2020 00:48:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:48:34: 11000000 INFO @ Sat, 27 Jun 2020 00:48:35: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:48:35: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:48:35: #1 total tags in treatment: 11245168 INFO @ Sat, 27 Jun 2020 00:48:35: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:48:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:48:36: #1 tags after filtering in treatment: 11245166 INFO @ Sat, 27 Jun 2020 00:48:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:48:36: #1 finished! INFO @ Sat, 27 Jun 2020 00:48:36: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:48:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:48:37: #2 number of paired peaks: 726 WARNING @ Sat, 27 Jun 2020 00:48:37: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Sat, 27 Jun 2020 00:48:37: start model_add_line... INFO @ Sat, 27 Jun 2020 00:48:37: start X-correlation... INFO @ Sat, 27 Jun 2020 00:48:37: end of X-cor INFO @ Sat, 27 Jun 2020 00:48:37: #2 finished! INFO @ Sat, 27 Jun 2020 00:48:37: #2 predicted fragment length is 46 bps INFO @ Sat, 27 Jun 2020 00:48:37: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sat, 27 Jun 2020 00:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.20_model.r WARNING @ Sat, 27 Jun 2020 00:48:37: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:48:37: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sat, 27 Jun 2020 00:48:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:48:37: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:48:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:48:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:48:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.10_summits.bed INFO @ Sat, 27 Jun 2020 00:48:43: Done! pass1 - making usageList (535 chroms): 1 millis pass2 - checking and writing primary data (2108 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:49:00: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:49:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:49:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:49:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX760382/SRX760382.20_summits.bed INFO @ Sat, 27 Jun 2020 00:49:11: Done! pass1 - making usageList (409 chroms): 1 millis pass2 - checking and writing primary data (1135 records, 4 fields): 13 millis CompletedMACS2peakCalling