Job ID = 6458618 SRX = SRX5343149 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:31:20 prefetch.2.10.7: 1) Downloading 'SRR8540849'... 2020-06-21T12:31:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:34:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:34:25 prefetch.2.10.7: 'SRR8540849' is valid 2020-06-21T12:34:25 prefetch.2.10.7: 1) 'SRR8540849' was downloaded successfully 2020-06-21T12:34:25 prefetch.2.10.7: 'SRR8540849' has 0 unresolved dependencies Read 17644335 spots for SRR8540849/SRR8540849.sra Written 17644335 spots for SRR8540849/SRR8540849.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: 00:04:21 17644335 reads; of these: 17644335 (100.00%) were unpaired; of these: 6785990 (38.46%) aligned 0 times 7837189 (44.42%) aligned exactly 1 time 3021156 (17.12%) aligned >1 times 61.54% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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] 4735294 / 10858345 = 0.4361 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 21:42:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.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 21:42:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:57: 1000000 INFO @ Sun, 21 Jun 2020 21:43:04: 2000000 INFO @ Sun, 21 Jun 2020 21:43:12: 3000000 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 21:43:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.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 21:43:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:43:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:43:20: 4000000 INFO @ Sun, 21 Jun 2020 21:43:27: 1000000 INFO @ Sun, 21 Jun 2020 21:43:28: 5000000 INFO @ Sun, 21 Jun 2020 21:43:35: 2000000 INFO @ Sun, 21 Jun 2020 21:43:37: 6000000 INFO @ Sun, 21 Jun 2020 21:43:38: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:43:38: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:43:38: #1 total tags in treatment: 6123051 INFO @ Sun, 21 Jun 2020 21:43:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:43:38: #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 21:43:38: #1 tags after filtering in treatment: 6123050 INFO @ Sun, 21 Jun 2020 21:43:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:43:38: #1 finished! INFO @ Sun, 21 Jun 2020 21:43:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:43:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:43:39: #2 number of paired peaks: 1299 INFO @ Sun, 21 Jun 2020 21:43:39: start model_add_line... INFO @ Sun, 21 Jun 2020 21:43:39: start X-correlation... INFO @ Sun, 21 Jun 2020 21:43:39: end of X-cor INFO @ Sun, 21 Jun 2020 21:43:39: #2 finished! INFO @ Sun, 21 Jun 2020 21:43:39: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:43:39: #2 alternative fragment length(s) may be 4,91 bps INFO @ Sun, 21 Jun 2020 21:43:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.05_model.r WARNING @ Sun, 21 Jun 2020 21:43:39: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:43:39: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Sun, 21 Jun 2020 21:43:39: #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 21:43:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:43:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:43:42: 3000000 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 21:43:49: 4000000 INFO @ Sun, 21 Jun 2020 21:43:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.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 21:43:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:43:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:43:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:56: 5000000 INFO @ Sun, 21 Jun 2020 21:43:58: 1000000 INFO @ Sun, 21 Jun 2020 21:43:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:43:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:43:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.05_summits.bed INFO @ Sun, 21 Jun 2020 21:43:59: Done! pass1 - making usageList (583 chroms): 1 millis pass2 - checking and writing primary data (1418 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:44:04: 6000000 INFO @ Sun, 21 Jun 2020 21:44:05: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:44:05: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:44:05: #1 total tags in treatment: 6123051 INFO @ Sun, 21 Jun 2020 21:44:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:44:05: #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 21:44:05: #1 tags after filtering in treatment: 6123050 INFO @ Sun, 21 Jun 2020 21:44:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:44:05: #1 finished! INFO @ Sun, 21 Jun 2020 21:44:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:44:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:44:06: #2 number of paired peaks: 1299 INFO @ Sun, 21 Jun 2020 21:44:06: start model_add_line... INFO @ Sun, 21 Jun 2020 21:44:06: start X-correlation... INFO @ Sun, 21 Jun 2020 21:44:06: end of X-cor INFO @ Sun, 21 Jun 2020 21:44:06: #2 finished! INFO @ Sun, 21 Jun 2020 21:44:06: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:44:06: #2 alternative fragment length(s) may be 4,91 bps INFO @ Sun, 21 Jun 2020 21:44:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.10_model.r WARNING @ Sun, 21 Jun 2020 21:44:06: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:44:06: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Sun, 21 Jun 2020 21:44:06: #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 21:44:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:44:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:44:06: 2000000 INFO @ Sun, 21 Jun 2020 21:44:14: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:44:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:44:22: 4000000 INFO @ Sun, 21 Jun 2020 21:44:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:44:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:44:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.10_summits.bed INFO @ Sun, 21 Jun 2020 21:44:26: Done! pass1 - making usageList (282 chroms): 1 millis pass2 - checking and writing primary data (590 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:44:30: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:44:38: 6000000 INFO @ Sun, 21 Jun 2020 21:44:39: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:44:39: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:44:39: #1 total tags in treatment: 6123051 INFO @ Sun, 21 Jun 2020 21:44:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:44:39: #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 21:44:39: #1 tags after filtering in treatment: 6123050 INFO @ Sun, 21 Jun 2020 21:44:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:44:39: #1 finished! INFO @ Sun, 21 Jun 2020 21:44:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:44:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:44:40: #2 number of paired peaks: 1299 INFO @ Sun, 21 Jun 2020 21:44:40: start model_add_line... INFO @ Sun, 21 Jun 2020 21:44:40: start X-correlation... INFO @ Sun, 21 Jun 2020 21:44:40: end of X-cor INFO @ Sun, 21 Jun 2020 21:44:40: #2 finished! INFO @ Sun, 21 Jun 2020 21:44:40: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:44:40: #2 alternative fragment length(s) may be 4,91 bps INFO @ Sun, 21 Jun 2020 21:44:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.20_model.r WARNING @ Sun, 21 Jun 2020 21:44:40: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:44:40: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Sun, 21 Jun 2020 21:44:40: #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 21:44:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:44:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:44:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:44:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:44:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:44:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343149/SRX5343149.20_summits.bed INFO @ Sun, 21 Jun 2020 21:44:58: Done! pass1 - making usageList (152 chroms): 1 millis pass2 - checking and writing primary data (302 records, 4 fields): 6 millis CompletedMACS2peakCalling