Job ID = 6458626 SRX = SRX5343157 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:44:40 prefetch.2.10.7: 1) Downloading 'SRR8540857'... 2020-06-21T12:44:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:48:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:48:22 prefetch.2.10.7: 1) 'SRR8540857' was downloaded successfully 2020-06-21T12:48:22 prefetch.2.10.7: 'SRR8540857' has 0 unresolved dependencies Read 21093528 spots for SRR8540857/SRR8540857.sra Written 21093528 spots for SRR8540857/SRR8540857.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: 00:00:01 Multiseed full-index search: 00:07:54 21093528 reads; of these: 21093528 (100.00%) were unpaired; of these: 1045318 (4.96%) aligned 0 times 13959517 (66.18%) aligned exactly 1 time 6088693 (28.87%) aligned >1 times 95.04% overall alignment rate Time searching: 00:07:55 Overall time: 00:07:55 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] 2875477 / 20048210 = 0.1434 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 22:03:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.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 22:03:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:17: 1000000 INFO @ Sun, 21 Jun 2020 22:03:22: 2000000 INFO @ Sun, 21 Jun 2020 22:03:27: 3000000 INFO @ Sun, 21 Jun 2020 22:03:32: 4000000 INFO @ Sun, 21 Jun 2020 22:03:38: 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 22:03:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.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 22:03:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:43: 6000000 INFO @ Sun, 21 Jun 2020 22:03:48: 7000000 INFO @ Sun, 21 Jun 2020 22:03:48: 1000000 INFO @ Sun, 21 Jun 2020 22:03:53: 8000000 INFO @ Sun, 21 Jun 2020 22:03:54: 2000000 INFO @ Sun, 21 Jun 2020 22:03:58: 9000000 INFO @ Sun, 21 Jun 2020 22:04:00: 3000000 INFO @ Sun, 21 Jun 2020 22:04:04: 10000000 INFO @ Sun, 21 Jun 2020 22:04:06: 4000000 INFO @ Sun, 21 Jun 2020 22:04:09: 11000000 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 22:04:11: 5000000 INFO @ Sun, 21 Jun 2020 22:04:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.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 22:04:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:14: 12000000 INFO @ Sun, 21 Jun 2020 22:04:17: 6000000 INFO @ Sun, 21 Jun 2020 22:04:18: 1000000 INFO @ Sun, 21 Jun 2020 22:04:19: 13000000 INFO @ Sun, 21 Jun 2020 22:04:23: 7000000 INFO @ Sun, 21 Jun 2020 22:04:24: 2000000 INFO @ Sun, 21 Jun 2020 22:04:24: 14000000 INFO @ Sun, 21 Jun 2020 22:04:29: 8000000 INFO @ Sun, 21 Jun 2020 22:04:29: 3000000 INFO @ Sun, 21 Jun 2020 22:04:30: 15000000 INFO @ Sun, 21 Jun 2020 22:04:35: 9000000 INFO @ Sun, 21 Jun 2020 22:04:35: 4000000 INFO @ Sun, 21 Jun 2020 22:04:35: 16000000 INFO @ Sun, 21 Jun 2020 22:04:41: 10000000 INFO @ Sun, 21 Jun 2020 22:04:41: 17000000 INFO @ Sun, 21 Jun 2020 22:04:41: 5000000 INFO @ Sun, 21 Jun 2020 22:04:42: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:04:42: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:04:42: #1 total tags in treatment: 17172733 INFO @ Sun, 21 Jun 2020 22:04:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:42: #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 22:04:42: #1 tags after filtering in treatment: 17172732 INFO @ Sun, 21 Jun 2020 22:04:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:42: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:43: #2 number of paired peaks: 285 WARNING @ Sun, 21 Jun 2020 22:04:43: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 21 Jun 2020 22:04:43: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:43: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:43: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:43: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:43: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 22:04:43: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sun, 21 Jun 2020 22:04:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.05_model.r WARNING @ Sun, 21 Jun 2020 22:04:43: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:43: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sun, 21 Jun 2020 22:04:43: #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 22:04:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:46: 11000000 INFO @ Sun, 21 Jun 2020 22:04:47: 6000000 INFO @ Sun, 21 Jun 2020 22:04:52: 12000000 INFO @ Sun, 21 Jun 2020 22:04:52: 7000000 INFO @ Sun, 21 Jun 2020 22:04:58: 13000000 INFO @ Sun, 21 Jun 2020 22:04:58: 8000000 INFO @ Sun, 21 Jun 2020 22:05:03: 14000000 INFO @ Sun, 21 Jun 2020 22:05:04: 9000000 INFO @ Sun, 21 Jun 2020 22:05:10: 15000000 INFO @ Sun, 21 Jun 2020 22:05:10: 10000000 INFO @ Sun, 21 Jun 2020 22:05:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:15: 11000000 INFO @ Sun, 21 Jun 2020 22:05:16: 16000000 INFO @ Sun, 21 Jun 2020 22:05:21: 12000000 INFO @ Sun, 21 Jun 2020 22:05:22: 17000000 INFO @ Sun, 21 Jun 2020 22:05:23: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:05:23: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:05:23: #1 total tags in treatment: 17172733 INFO @ Sun, 21 Jun 2020 22:05:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:23: #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 22:05:23: #1 tags after filtering in treatment: 17172732 INFO @ Sun, 21 Jun 2020 22:05:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:23: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:24: #2 number of paired peaks: 285 WARNING @ Sun, 21 Jun 2020 22:05:24: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:24: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:25: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:25: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:25: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:25: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 22:05:25: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sun, 21 Jun 2020 22:05:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.10_model.r WARNING @ Sun, 21 Jun 2020 22:05:25: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:25: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sun, 21 Jun 2020 22:05:25: #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 22:05:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:27: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:05:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.05_summits.bed INFO @ Sun, 21 Jun 2020 22:05:30: Done! pass1 - making usageList (697 chroms): 1 millis pass2 - checking and writing primary data (2332 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:05:32: 14000000 INFO @ Sun, 21 Jun 2020 22:05:39: 15000000 INFO @ Sun, 21 Jun 2020 22:05:45: 16000000 INFO @ Sun, 21 Jun 2020 22:05:51: 17000000 INFO @ Sun, 21 Jun 2020 22:05:52: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:05:52: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:05:52: #1 total tags in treatment: 17172733 INFO @ Sun, 21 Jun 2020 22:05:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:52: #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 22:05:52: #1 tags after filtering in treatment: 17172732 INFO @ Sun, 21 Jun 2020 22:05:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:52: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:54: #2 number of paired peaks: 285 WARNING @ Sun, 21 Jun 2020 22:05:54: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:54: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:54: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:54: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:54: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:54: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 22:05:54: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sun, 21 Jun 2020 22:05:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.20_model.r WARNING @ Sun, 21 Jun 2020 22:05:54: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:54: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sun, 21 Jun 2020 22:05:54: #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 22:05:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:06:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.10_summits.bed INFO @ Sun, 21 Jun 2020 22:06:11: Done! pass1 - making usageList (522 chroms): 1 millis pass2 - checking and writing primary data (1502 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:06:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:06:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343157/SRX5343157.20_summits.bed INFO @ Sun, 21 Jun 2020 22:06:39: Done! pass1 - making usageList (287 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 8 millis CompletedMACS2peakCalling