Job ID = 6457865 SRX = SRX4823781 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:03:34 prefetch.2.10.7: 1) Downloading 'SRR7992739'... 2020-06-21T12:03:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:08:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:08:14 prefetch.2.10.7: 1) 'SRR7992739' was downloaded successfully 2020-06-21T12:08:14 prefetch.2.10.7: 'SRR7992739' has 0 unresolved dependencies Read 35147143 spots for SRR7992739/SRR7992739.sra Written 35147143 spots for SRR7992739/SRR7992739.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: 00:11:22 35147143 reads; of these: 35147143 (100.00%) were unpaired; of these: 4073549 (11.59%) aligned 0 times 20218177 (57.52%) aligned exactly 1 time 10855417 (30.89%) aligned >1 times 88.41% overall alignment rate Time searching: 00:11:22 Overall time: 00:11:22 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] 20489471 / 31073594 = 0.6594 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 21:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.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 21:26:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:24: 1000000 INFO @ Sun, 21 Jun 2020 21:26:30: 2000000 INFO @ Sun, 21 Jun 2020 21:26:37: 3000000 INFO @ Sun, 21 Jun 2020 21:26:43: 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 21:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.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 21:26:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:50: 5000000 INFO @ Sun, 21 Jun 2020 21:26:54: 1000000 INFO @ Sun, 21 Jun 2020 21:26:57: 6000000 INFO @ Sun, 21 Jun 2020 21:27:02: 2000000 INFO @ Sun, 21 Jun 2020 21:27:05: 7000000 INFO @ Sun, 21 Jun 2020 21:27:09: 3000000 INFO @ Sun, 21 Jun 2020 21:27:12: 8000000 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 21:27:16: 4000000 INFO @ Sun, 21 Jun 2020 21:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.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 21:27:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:19: 9000000 INFO @ Sun, 21 Jun 2020 21:27:23: 5000000 INFO @ Sun, 21 Jun 2020 21:27:24: 1000000 INFO @ Sun, 21 Jun 2020 21:27:27: 10000000 INFO @ Sun, 21 Jun 2020 21:27:30: 6000000 INFO @ Sun, 21 Jun 2020 21:27:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:27:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:27:31: #1 total tags in treatment: 10584123 INFO @ Sun, 21 Jun 2020 21:27:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:27:31: #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 21:27:31: #1 tags after filtering in treatment: 10584042 INFO @ Sun, 21 Jun 2020 21:27:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:27:31: #1 finished! INFO @ Sun, 21 Jun 2020 21:27:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:27:32: 2000000 INFO @ Sun, 21 Jun 2020 21:27:32: #2 number of paired peaks: 1923 INFO @ Sun, 21 Jun 2020 21:27:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:27:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:27:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:27:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:27:32: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 21:27:32: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 21 Jun 2020 21:27:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.05_model.r WARNING @ Sun, 21 Jun 2020 21:27:32: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:27:32: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 21 Jun 2020 21:27:32: #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 21:27:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:27:38: 7000000 INFO @ Sun, 21 Jun 2020 21:27:39: 3000000 INFO @ Sun, 21 Jun 2020 21:27:45: 8000000 INFO @ Sun, 21 Jun 2020 21:27:46: 4000000 INFO @ Sun, 21 Jun 2020 21:27:52: 9000000 INFO @ Sun, 21 Jun 2020 21:27:53: 5000000 INFO @ Sun, 21 Jun 2020 21:27:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:28:00: 10000000 INFO @ Sun, 21 Jun 2020 21:28:01: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:28:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:04: #1 total tags in treatment: 10584123 INFO @ Sun, 21 Jun 2020 21:28:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:04: #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 21:28:04: #1 tags after filtering in treatment: 10584042 INFO @ Sun, 21 Jun 2020 21:28:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:05: #2 number of paired peaks: 1923 INFO @ Sun, 21 Jun 2020 21:28:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:05: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 21:28:05: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 21 Jun 2020 21:28:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.10_model.r WARNING @ Sun, 21 Jun 2020 21:28:05: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:28:05: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 21 Jun 2020 21:28:05: #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 21:28:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:28:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:28:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:28:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.05_summits.bed INFO @ Sun, 21 Jun 2020 21:28:07: Done! pass1 - making usageList (800 chroms): 2 millis pass2 - checking and writing primary data (5160 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:28:07: 7000000 INFO @ Sun, 21 Jun 2020 21:28:14: 8000000 INFO @ Sun, 21 Jun 2020 21:28:20: 9000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:28:27: 10000000 INFO @ Sun, 21 Jun 2020 21:28:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:28:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:31: #1 total tags in treatment: 10584123 INFO @ Sun, 21 Jun 2020 21:28:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:31: #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 21:28:31: #1 tags after filtering in treatment: 10584042 INFO @ Sun, 21 Jun 2020 21:28:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:31: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:32: #2 number of paired peaks: 1923 INFO @ Sun, 21 Jun 2020 21:28:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:32: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 21:28:32: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 21 Jun 2020 21:28:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.20_model.r WARNING @ Sun, 21 Jun 2020 21:28:32: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:28:32: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 21 Jun 2020 21:28:32: #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 21:28:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:28:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:28:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:28:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.10_summits.bed INFO @ Sun, 21 Jun 2020 21:28:39: Done! pass1 - making usageList (672 chroms): 1 millis pass2 - checking and writing primary data (3167 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:28:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823781/SRX4823781.20_summits.bed INFO @ Sun, 21 Jun 2020 21:29:04: Done! pass1 - making usageList (582 chroms): 1 millis pass2 - checking and writing primary data (2063 records, 4 fields): 18 millis CompletedMACS2peakCalling