Job ID = 6458837 SRX = SRX5661483 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:44:56 prefetch.2.10.7: 1) Downloading 'SRR8874490'... 2020-06-21T12:44:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:48:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:48:50 prefetch.2.10.7: 1) 'SRR8874490' was downloaded successfully 2020-06-21T12:48:50 prefetch.2.10.7: 'SRR8874490' has 0 unresolved dependencies Read 33781979 spots for SRR8874490/SRR8874490.sra Written 33781979 spots for SRR8874490/SRR8874490.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: 00:10:46 33781979 reads; of these: 33781979 (100.00%) were unpaired; of these: 3604748 (10.67%) aligned 0 times 21838852 (64.65%) aligned exactly 1 time 8338379 (24.68%) aligned >1 times 89.33% overall alignment rate Time searching: 00:10:46 Overall time: 00:10:46 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 16 files... [bam_rmdupse_core] 14872734 / 30177231 = 0.4928 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 22:06:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.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 22:06:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:01: 1000000 INFO @ Sun, 21 Jun 2020 22:07:06: 2000000 INFO @ Sun, 21 Jun 2020 22:07:12: 3000000 INFO @ Sun, 21 Jun 2020 22:07:17: 4000000 INFO @ Sun, 21 Jun 2020 22:07:23: 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 22:07:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.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 22:07:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:29: 6000000 INFO @ Sun, 21 Jun 2020 22:07:31: 1000000 INFO @ Sun, 21 Jun 2020 22:07:35: 7000000 INFO @ Sun, 21 Jun 2020 22:07:37: 2000000 INFO @ Sun, 21 Jun 2020 22:07:42: 8000000 INFO @ Sun, 21 Jun 2020 22:07:43: 3000000 INFO @ Sun, 21 Jun 2020 22:07:48: 9000000 INFO @ Sun, 21 Jun 2020 22:07:49: 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 22:07:54: 10000000 INFO @ Sun, 21 Jun 2020 22:07:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.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 22:07:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:55: 5000000 INFO @ Sun, 21 Jun 2020 22:08:00: 11000000 INFO @ Sun, 21 Jun 2020 22:08:01: 1000000 INFO @ Sun, 21 Jun 2020 22:08:01: 6000000 INFO @ Sun, 21 Jun 2020 22:08:06: 12000000 INFO @ Sun, 21 Jun 2020 22:08:07: 2000000 INFO @ Sun, 21 Jun 2020 22:08:07: 7000000 INFO @ Sun, 21 Jun 2020 22:08:13: 3000000 INFO @ Sun, 21 Jun 2020 22:08:13: 13000000 INFO @ Sun, 21 Jun 2020 22:08:13: 8000000 INFO @ Sun, 21 Jun 2020 22:08:19: 9000000 INFO @ Sun, 21 Jun 2020 22:08:19: 4000000 INFO @ Sun, 21 Jun 2020 22:08:19: 14000000 INFO @ Sun, 21 Jun 2020 22:08:24: 5000000 INFO @ Sun, 21 Jun 2020 22:08:25: 10000000 INFO @ Sun, 21 Jun 2020 22:08:25: 15000000 INFO @ Sun, 21 Jun 2020 22:08:27: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:08:27: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:08:27: #1 total tags in treatment: 15304497 INFO @ Sun, 21 Jun 2020 22:08:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:08:27: #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 22:08:28: #1 tags after filtering in treatment: 15304492 INFO @ Sun, 21 Jun 2020 22:08:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:08:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:08:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:08:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:08:29: #2 number of paired peaks: 679 WARNING @ Sun, 21 Jun 2020 22:08:29: Fewer paired peaks (679) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 679 pairs to build model! INFO @ Sun, 21 Jun 2020 22:08:29: start model_add_line... INFO @ Sun, 21 Jun 2020 22:08:29: start X-correlation... INFO @ Sun, 21 Jun 2020 22:08:29: end of X-cor INFO @ Sun, 21 Jun 2020 22:08:29: #2 finished! INFO @ Sun, 21 Jun 2020 22:08:29: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 22:08:29: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sun, 21 Jun 2020 22:08:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.05_model.r WARNING @ Sun, 21 Jun 2020 22:08:29: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:08:29: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sun, 21 Jun 2020 22:08:29: #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 22:08:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:08:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:08:30: 11000000 INFO @ Sun, 21 Jun 2020 22:08:30: 6000000 INFO @ Sun, 21 Jun 2020 22:08:36: 7000000 INFO @ Sun, 21 Jun 2020 22:08:36: 12000000 INFO @ Sun, 21 Jun 2020 22:08:42: 8000000 INFO @ Sun, 21 Jun 2020 22:08:43: 13000000 INFO @ Sun, 21 Jun 2020 22:08:48: 9000000 INFO @ Sun, 21 Jun 2020 22:08:48: 14000000 INFO @ Sun, 21 Jun 2020 22:08:54: 10000000 INFO @ Sun, 21 Jun 2020 22:08:54: 15000000 INFO @ Sun, 21 Jun 2020 22:08:56: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:08:56: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:08:56: #1 total tags in treatment: 15304497 INFO @ Sun, 21 Jun 2020 22:08:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:08:56: #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 22:08:57: #1 tags after filtering in treatment: 15304492 INFO @ Sun, 21 Jun 2020 22:08:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:08:57: #1 finished! INFO @ Sun, 21 Jun 2020 22:08:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:08:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:08:58: #2 number of paired peaks: 679 WARNING @ Sun, 21 Jun 2020 22:08:58: Fewer paired peaks (679) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 679 pairs to build model! INFO @ Sun, 21 Jun 2020 22:08:58: start model_add_line... INFO @ Sun, 21 Jun 2020 22:08:58: start X-correlation... INFO @ Sun, 21 Jun 2020 22:08:58: end of X-cor INFO @ Sun, 21 Jun 2020 22:08:58: #2 finished! INFO @ Sun, 21 Jun 2020 22:08:58: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 22:08:58: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sun, 21 Jun 2020 22:08:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.10_model.r WARNING @ Sun, 21 Jun 2020 22:08:58: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:08:58: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sun, 21 Jun 2020 22:08:58: #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 22:08:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:08:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:08:59: 11000000 INFO @ Sun, 21 Jun 2020 22:09:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:09:05: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:09:11: 13000000 INFO @ Sun, 21 Jun 2020 22:09:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:09:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:09:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.05_summits.bed INFO @ Sun, 21 Jun 2020 22:09:16: Done! INFO @ Sun, 21 Jun 2020 22:09:16: 14000000 pass1 - making usageList (823 chroms): 2 millis pass2 - checking and writing primary data (3552 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:09:22: 15000000 INFO @ Sun, 21 Jun 2020 22:09:24: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:09:24: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:09:24: #1 total tags in treatment: 15304497 INFO @ Sun, 21 Jun 2020 22:09:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:09:24: #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 22:09:24: #1 tags after filtering in treatment: 15304492 INFO @ Sun, 21 Jun 2020 22:09:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:09:24: #1 finished! INFO @ Sun, 21 Jun 2020 22:09:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:09:25: #2 number of paired peaks: 679 WARNING @ Sun, 21 Jun 2020 22:09:25: Fewer paired peaks (679) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 679 pairs to build model! INFO @ Sun, 21 Jun 2020 22:09:25: start model_add_line... INFO @ Sun, 21 Jun 2020 22:09:25: start X-correlation... INFO @ Sun, 21 Jun 2020 22:09:25: end of X-cor INFO @ Sun, 21 Jun 2020 22:09:25: #2 finished! INFO @ Sun, 21 Jun 2020 22:09:25: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 22:09:25: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sun, 21 Jun 2020 22:09:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.20_model.r WARNING @ Sun, 21 Jun 2020 22:09:25: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:09:25: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sun, 21 Jun 2020 22:09:25: #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 22:09:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:09:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:09:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:09:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:09:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:09:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.10_summits.bed INFO @ Sun, 21 Jun 2020 22:09:43: Done! pass1 - making usageList (652 chroms): 1 millis pass2 - checking and writing primary data (2416 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:09:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:10:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:10:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:10:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661483/SRX5661483.20_summits.bed INFO @ Sun, 21 Jun 2020 22:10:11: Done! pass1 - making usageList (494 chroms): 1 millis pass2 - checking and writing primary data (1197 records, 4 fields): 14 millis CompletedMACS2peakCalling