Job ID = 6453151 SRX = SRX104973 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:02:53 prefetch.2.10.7: 1) Downloading 'SRR363417'... 2020-06-21T08:02:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:11:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:11:47 prefetch.2.10.7: 1) 'SRR363417' was downloaded successfully Read 39814481 spots for SRR363417/SRR363417.sra Written 39814481 spots for SRR363417/SRR363417.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: 00:07:30 39814481 reads; of these: 39814481 (100.00%) were unpaired; of these: 3375261 (8.48%) aligned 0 times 29693917 (74.58%) aligned exactly 1 time 6745303 (16.94%) aligned >1 times 91.52% overall alignment rate Time searching: 00:07:30 Overall time: 00:07:30 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] 15145696 / 36439220 = 0.4156 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 17:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.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 17:30:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:10: 1000000 INFO @ Sun, 21 Jun 2020 17:30:15: 2000000 INFO @ Sun, 21 Jun 2020 17:30:19: 3000000 INFO @ Sun, 21 Jun 2020 17:30:24: 4000000 INFO @ Sun, 21 Jun 2020 17:30:29: 5000000 INFO @ Sun, 21 Jun 2020 17:30:33: 6000000 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 17:30:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.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 17:30:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:38: 7000000 INFO @ Sun, 21 Jun 2020 17:30:41: 1000000 INFO @ Sun, 21 Jun 2020 17:30:43: 8000000 INFO @ Sun, 21 Jun 2020 17:30:46: 2000000 INFO @ Sun, 21 Jun 2020 17:30:48: 9000000 INFO @ Sun, 21 Jun 2020 17:30:51: 3000000 INFO @ Sun, 21 Jun 2020 17:30:53: 10000000 INFO @ Sun, 21 Jun 2020 17:30:56: 4000000 INFO @ Sun, 21 Jun 2020 17:30:58: 11000000 INFO @ Sun, 21 Jun 2020 17:31:02: 5000000 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 17:31:03: 12000000 INFO @ Sun, 21 Jun 2020 17:31:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.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 17:31:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:07: 6000000 INFO @ Sun, 21 Jun 2020 17:31:08: 13000000 INFO @ Sun, 21 Jun 2020 17:31:10: 1000000 INFO @ Sun, 21 Jun 2020 17:31:12: 7000000 INFO @ Sun, 21 Jun 2020 17:31:13: 14000000 INFO @ Sun, 21 Jun 2020 17:31:15: 2000000 INFO @ Sun, 21 Jun 2020 17:31:17: 8000000 INFO @ Sun, 21 Jun 2020 17:31:19: 15000000 INFO @ Sun, 21 Jun 2020 17:31:20: 3000000 INFO @ Sun, 21 Jun 2020 17:31:22: 9000000 INFO @ Sun, 21 Jun 2020 17:31:24: 16000000 INFO @ Sun, 21 Jun 2020 17:31:25: 4000000 INFO @ Sun, 21 Jun 2020 17:31:28: 10000000 INFO @ Sun, 21 Jun 2020 17:31:29: 17000000 INFO @ Sun, 21 Jun 2020 17:31:30: 5000000 INFO @ Sun, 21 Jun 2020 17:31:33: 11000000 INFO @ Sun, 21 Jun 2020 17:31:35: 6000000 INFO @ Sun, 21 Jun 2020 17:31:35: 18000000 INFO @ Sun, 21 Jun 2020 17:31:38: 12000000 INFO @ Sun, 21 Jun 2020 17:31:40: 7000000 INFO @ Sun, 21 Jun 2020 17:31:41: 19000000 INFO @ Sun, 21 Jun 2020 17:31:43: 13000000 INFO @ Sun, 21 Jun 2020 17:31:45: 8000000 INFO @ Sun, 21 Jun 2020 17:31:46: 20000000 INFO @ Sun, 21 Jun 2020 17:31:48: 14000000 INFO @ Sun, 21 Jun 2020 17:31:49: 9000000 INFO @ Sun, 21 Jun 2020 17:31:52: 21000000 INFO @ Sun, 21 Jun 2020 17:31:54: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:31:54: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:31:54: #1 total tags in treatment: 21293524 INFO @ Sun, 21 Jun 2020 17:31:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:54: #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 17:31:54: 15000000 INFO @ Sun, 21 Jun 2020 17:31:54: 10000000 INFO @ Sun, 21 Jun 2020 17:31:55: #1 tags after filtering in treatment: 21293520 INFO @ Sun, 21 Jun 2020 17:31:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:55: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:56: #2 number of paired peaks: 395 WARNING @ Sun, 21 Jun 2020 17:31:56: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 21 Jun 2020 17:31:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:56: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:56: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:56: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:56: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 17:31:56: #2 alternative fragment length(s) may be 3,46,575 bps INFO @ Sun, 21 Jun 2020 17:31:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.05_model.r WARNING @ Sun, 21 Jun 2020 17:31:56: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:31:56: #2 You may need to consider one of the other alternative d(s): 3,46,575 WARNING @ Sun, 21 Jun 2020 17:31:56: #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 17:31:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:59: 16000000 INFO @ Sun, 21 Jun 2020 17:32:00: 11000000 INFO @ Sun, 21 Jun 2020 17:32:04: 17000000 INFO @ Sun, 21 Jun 2020 17:32:04: 12000000 INFO @ Sun, 21 Jun 2020 17:32:09: 13000000 INFO @ Sun, 21 Jun 2020 17:32:09: 18000000 INFO @ Sun, 21 Jun 2020 17:32:14: 14000000 INFO @ Sun, 21 Jun 2020 17:32:14: 19000000 INFO @ Sun, 21 Jun 2020 17:32:18: 15000000 INFO @ Sun, 21 Jun 2020 17:32:19: 20000000 INFO @ Sun, 21 Jun 2020 17:32:23: 16000000 INFO @ Sun, 21 Jun 2020 17:32:24: 21000000 INFO @ Sun, 21 Jun 2020 17:32:26: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:32:26: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:32:26: #1 total tags in treatment: 21293524 INFO @ Sun, 21 Jun 2020 17:32:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:32:26: #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 17:32:27: #1 tags after filtering in treatment: 21293520 INFO @ Sun, 21 Jun 2020 17:32:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:32:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:32:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:32:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:32:28: 17000000 INFO @ Sun, 21 Jun 2020 17:32:28: #2 number of paired peaks: 395 WARNING @ Sun, 21 Jun 2020 17:32:28: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 21 Jun 2020 17:32:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:32:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:32:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:32:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:32:28: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 17:32:28: #2 alternative fragment length(s) may be 3,46,575 bps INFO @ Sun, 21 Jun 2020 17:32:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.10_model.r WARNING @ Sun, 21 Jun 2020 17:32:28: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:32:28: #2 You may need to consider one of the other alternative d(s): 3,46,575 WARNING @ Sun, 21 Jun 2020 17:32:28: #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 17:32:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:32:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:32:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:32:33: 18000000 INFO @ Sun, 21 Jun 2020 17:32:38: 19000000 INFO @ Sun, 21 Jun 2020 17:32:43: 20000000 INFO @ Sun, 21 Jun 2020 17:32:48: 21000000 INFO @ Sun, 21 Jun 2020 17:32:49: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:32:49: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:32:49: #1 total tags in treatment: 21293524 INFO @ Sun, 21 Jun 2020 17:32:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:32:49: #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 17:32:50: #1 tags after filtering in treatment: 21293520 INFO @ Sun, 21 Jun 2020 17:32:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:32:50: #1 finished! INFO @ Sun, 21 Jun 2020 17:32:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:32:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:32:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.05_summits.bed INFO @ Sun, 21 Jun 2020 17:32:51: Done! pass1 - making usageList (487 chroms): 2 millis pass2 - checking and writing primary data (4245 records, 4 fields): 82 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:32:52: #2 number of paired peaks: 395 WARNING @ Sun, 21 Jun 2020 17:32:52: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 21 Jun 2020 17:32:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:32:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:32:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:32:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:32:52: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 17:32:52: #2 alternative fragment length(s) may be 3,46,575 bps INFO @ Sun, 21 Jun 2020 17:32:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.20_model.r WARNING @ Sun, 21 Jun 2020 17:32:52: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:32:52: #2 You may need to consider one of the other alternative d(s): 3,46,575 WARNING @ Sun, 21 Jun 2020 17:32:52: #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 17:32:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:32:52: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:33:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:33:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:33:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:33:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.10_summits.bed INFO @ Sun, 21 Jun 2020 17:33:23: Done! pass1 - making usageList (386 chroms): 1 millis pass2 - checking and writing primary data (1999 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:33:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:33:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:33:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:33:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104973/SRX104973.20_summits.bed INFO @ Sun, 21 Jun 2020 17:33:47: Done! pass1 - making usageList (119 chroms): 1 millis pass2 - checking and writing primary data (455 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。