Job ID = 6456612 SRX = SRX372806 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:01:01 prefetch.2.10.7: 1) Downloading 'SRR1023762'... 2020-06-21T11:01:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:03:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:03:08 prefetch.2.10.7: 1) 'SRR1023762' was downloaded successfully Read 19903332 spots for SRR1023762/SRR1023762.sra Written 19903332 spots for SRR1023762/SRR1023762.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: 00:05:34 19903332 reads; of these: 19903332 (100.00%) were unpaired; of these: 897721 (4.51%) aligned 0 times 12836208 (64.49%) aligned exactly 1 time 6169403 (31.00%) aligned >1 times 95.49% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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] 7781716 / 19005611 = 0.4094 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 20:14:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.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 20:14:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:29: 1000000 INFO @ Sun, 21 Jun 2020 20:14:34: 2000000 INFO @ Sun, 21 Jun 2020 20:14:40: 3000000 INFO @ Sun, 21 Jun 2020 20:14:46: 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 @ Sun, 21 Jun 2020 20:14:51: 5000000 INFO @ Sun, 21 Jun 2020 20:14:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.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 20:14:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:58: 6000000 INFO @ Sun, 21 Jun 2020 20:14:59: 1000000 INFO @ Sun, 21 Jun 2020 20:15:04: 7000000 INFO @ Sun, 21 Jun 2020 20:15:05: 2000000 INFO @ Sun, 21 Jun 2020 20:15:10: 8000000 INFO @ Sun, 21 Jun 2020 20:15:12: 3000000 INFO @ Sun, 21 Jun 2020 20:15:17: 9000000 INFO @ Sun, 21 Jun 2020 20:15:18: 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 20:15:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.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 20:15:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:15:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:15:23: 10000000 INFO @ Sun, 21 Jun 2020 20:15:24: 5000000 INFO @ Sun, 21 Jun 2020 20:15:29: 1000000 INFO @ Sun, 21 Jun 2020 20:15:29: 11000000 INFO @ Sun, 21 Jun 2020 20:15:31: 6000000 INFO @ Sun, 21 Jun 2020 20:15:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:15:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:15:31: #1 total tags in treatment: 11223895 INFO @ Sun, 21 Jun 2020 20:15:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:15:31: #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 20:15:31: #1 tags after filtering in treatment: 11223894 INFO @ Sun, 21 Jun 2020 20:15:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:15:31: #1 finished! INFO @ Sun, 21 Jun 2020 20:15:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:15:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:15:32: #2 number of paired peaks: 1163 INFO @ Sun, 21 Jun 2020 20:15:32: start model_add_line... INFO @ Sun, 21 Jun 2020 20:15:32: start X-correlation... INFO @ Sun, 21 Jun 2020 20:15:32: end of X-cor INFO @ Sun, 21 Jun 2020 20:15:32: #2 finished! INFO @ Sun, 21 Jun 2020 20:15:32: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 20:15:32: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sun, 21 Jun 2020 20:15:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.05_model.r WARNING @ Sun, 21 Jun 2020 20:15:32: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:15:32: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sun, 21 Jun 2020 20:15:32: #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 20:15:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:15:35: 2000000 INFO @ Sun, 21 Jun 2020 20:15:37: 7000000 INFO @ Sun, 21 Jun 2020 20:15:42: 3000000 INFO @ Sun, 21 Jun 2020 20:15:43: 8000000 INFO @ Sun, 21 Jun 2020 20:15:48: 4000000 INFO @ Sun, 21 Jun 2020 20:15:50: 9000000 INFO @ Sun, 21 Jun 2020 20:15:54: 5000000 INFO @ Sun, 21 Jun 2020 20:15:56: 10000000 INFO @ Sun, 21 Jun 2020 20:15:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:16:01: 6000000 INFO @ Sun, 21 Jun 2020 20:16:02: 11000000 INFO @ Sun, 21 Jun 2020 20:16:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:16:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:16:04: #1 total tags in treatment: 11223895 INFO @ Sun, 21 Jun 2020 20:16:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:04: #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 20:16:04: #1 tags after filtering in treatment: 11223894 INFO @ Sun, 21 Jun 2020 20:16:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:16:04: #1 finished! INFO @ Sun, 21 Jun 2020 20:16:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:16:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:16:05: #2 number of paired peaks: 1163 INFO @ Sun, 21 Jun 2020 20:16:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:16:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:16:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:16:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:16:05: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 20:16:05: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sun, 21 Jun 2020 20:16:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.10_model.r WARNING @ Sun, 21 Jun 2020 20:16:05: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:16:05: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sun, 21 Jun 2020 20:16:05: #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 20:16:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:16:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:16:07: 7000000 INFO @ Sun, 21 Jun 2020 20:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.05_summits.bed INFO @ Sun, 21 Jun 2020 20:16:08: Done! pass1 - making usageList (772 chroms): 1 millis pass2 - checking and writing primary data (4272 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:16:13: 8000000 INFO @ Sun, 21 Jun 2020 20:16:19: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:16:24: 10000000 INFO @ Sun, 21 Jun 2020 20:16:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:16:30: 11000000 INFO @ Sun, 21 Jun 2020 20:16:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:16:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:16:31: #1 total tags in treatment: 11223895 INFO @ Sun, 21 Jun 2020 20:16:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:31: #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 20:16:32: #1 tags after filtering in treatment: 11223894 INFO @ Sun, 21 Jun 2020 20:16:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:16:32: #1 finished! INFO @ Sun, 21 Jun 2020 20:16:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:16:33: #2 number of paired peaks: 1163 INFO @ Sun, 21 Jun 2020 20:16:33: start model_add_line... INFO @ Sun, 21 Jun 2020 20:16:33: start X-correlation... INFO @ Sun, 21 Jun 2020 20:16:33: end of X-cor INFO @ Sun, 21 Jun 2020 20:16:33: #2 finished! INFO @ Sun, 21 Jun 2020 20:16:33: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 20:16:33: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sun, 21 Jun 2020 20:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.20_model.r WARNING @ Sun, 21 Jun 2020 20:16:33: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:16:33: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sun, 21 Jun 2020 20:16:33: #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 20:16:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:16:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.10_summits.bed INFO @ Sun, 21 Jun 2020 20:16:41: Done! pass1 - making usageList (626 chroms): 2 millis pass2 - checking and writing primary data (2769 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:16:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:17:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:17:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:17:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX372806/SRX372806.20_summits.bed INFO @ Sun, 21 Jun 2020 20:17:08: Done! pass1 - making usageList (479 chroms): 1 millis pass2 - checking and writing primary data (1420 records, 4 fields): 15 millis CompletedMACS2peakCalling