Job ID = 6458448 SRX = SRX5227002 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:28:22 prefetch.2.10.7: 1) Downloading 'SRR8417917'... 2020-06-21T12:28:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:31:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:31:31 prefetch.2.10.7: 'SRR8417917' is valid 2020-06-21T12:31:31 prefetch.2.10.7: 1) 'SRR8417917' was downloaded successfully 2020-06-21T12:31:31 prefetch.2.10.7: 'SRR8417917' has 0 unresolved dependencies Read 11293501 spots for SRR8417917/SRR8417917.sra Written 11293501 spots for SRR8417917/SRR8417917.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: 00:03:46 11293501 reads; of these: 11293501 (100.00%) were unpaired; of these: 602367 (5.33%) aligned 0 times 7870783 (69.69%) aligned exactly 1 time 2820351 (24.97%) aligned >1 times 94.67% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 1020455 / 10691134 = 0.0954 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 21:39:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.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 21:39:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:39:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:39:52: 1000000 INFO @ Sun, 21 Jun 2020 21:39:57: 2000000 INFO @ Sun, 21 Jun 2020 21:40:03: 3000000 INFO @ Sun, 21 Jun 2020 21:40:09: 4000000 INFO @ Sun, 21 Jun 2020 21:40:14: 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 21:40:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.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 21:40:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:20: 6000000 INFO @ Sun, 21 Jun 2020 21:40:23: 1000000 INFO @ Sun, 21 Jun 2020 21:40:27: 7000000 INFO @ Sun, 21 Jun 2020 21:40:30: 2000000 INFO @ Sun, 21 Jun 2020 21:40:33: 8000000 INFO @ Sun, 21 Jun 2020 21:40:37: 3000000 INFO @ Sun, 21 Jun 2020 21:40:40: 9000000 INFO @ Sun, 21 Jun 2020 21:40:44: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:40:44: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:40:44: #1 total tags in treatment: 9670679 INFO @ Sun, 21 Jun 2020 21:40:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 21:40:45: 4000000 INFO @ Sun, 21 Jun 2020 21:40:45: #1 tags after filtering in treatment: 9670506 INFO @ Sun, 21 Jun 2020 21:40:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:45: #2 number of paired peaks: 1242 INFO @ Sun, 21 Jun 2020 21:40:45: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:45: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:45: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:45: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:45: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 21:40:45: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 21:40:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.05_model.r WARNING @ Sun, 21 Jun 2020 21:40:45: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:40:45: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sun, 21 Jun 2020 21:40:45: #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 21:40:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:40:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.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 21:40:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:52: 5000000 INFO @ Sun, 21 Jun 2020 21:40:53: 1000000 INFO @ Sun, 21 Jun 2020 21:40:59: 6000000 INFO @ Sun, 21 Jun 2020 21:41:00: 2000000 INFO @ Sun, 21 Jun 2020 21:41:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:06: 3000000 INFO @ Sun, 21 Jun 2020 21:41:07: 7000000 INFO @ Sun, 21 Jun 2020 21:41:13: 4000000 INFO @ Sun, 21 Jun 2020 21:41:14: 8000000 INFO @ Sun, 21 Jun 2020 21:41:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.05_summits.bed INFO @ Sun, 21 Jun 2020 21:41:16: Done! pass1 - making usageList (428 chroms): 1 millis pass2 - checking and writing primary data (3696 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:41:19: 5000000 INFO @ Sun, 21 Jun 2020 21:41:22: 9000000 INFO @ Sun, 21 Jun 2020 21:41:26: 6000000 INFO @ Sun, 21 Jun 2020 21:41:27: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:41:27: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:41:27: #1 total tags in treatment: 9670679 INFO @ Sun, 21 Jun 2020 21:41:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:27: #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 21:41:27: #1 tags after filtering in treatment: 9670506 INFO @ Sun, 21 Jun 2020 21:41:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:28: #2 number of paired peaks: 1242 INFO @ Sun, 21 Jun 2020 21:41:28: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:28: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 21:41:28: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 21:41:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.10_model.r WARNING @ Sun, 21 Jun 2020 21:41:28: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:41:28: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sun, 21 Jun 2020 21:41:28: #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 21:41:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:32: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:41:38: 8000000 INFO @ Sun, 21 Jun 2020 21:41:44: 9000000 INFO @ Sun, 21 Jun 2020 21:41:48: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:41:48: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:41:48: #1 total tags in treatment: 9670679 INFO @ Sun, 21 Jun 2020 21:41:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:48: #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 21:41:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:49: #1 tags after filtering in treatment: 9670506 INFO @ Sun, 21 Jun 2020 21:41:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:49: #2 number of paired peaks: 1242 INFO @ Sun, 21 Jun 2020 21:41:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:50: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:50: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:50: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 21:41:50: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 21:41:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.20_model.r WARNING @ Sun, 21 Jun 2020 21:41:50: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:41:50: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sun, 21 Jun 2020 21:41:50: #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 21:41:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:41:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.10_summits.bed INFO @ Sun, 21 Jun 2020 21:41:59: Done! pass1 - making usageList (318 chroms): 1 millis pass2 - checking and writing primary data (1675 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:42:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227002/SRX5227002.20_summits.bed INFO @ Sun, 21 Jun 2020 21:42:20: Done! pass1 - making usageList (197 chroms): 0 millis pass2 - checking and writing primary data (637 records, 4 fields): 7 millis CompletedMACS2peakCalling