Job ID = 6457945 SRX = SRX4923189 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:05:51 prefetch.2.10.7: 1) Downloading 'SRR8096339'... 2020-06-21T12:05:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:08:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:08:29 prefetch.2.10.7: 1) 'SRR8096339' was downloaded successfully 2020-06-21T12:08:29 prefetch.2.10.7: 'SRR8096339' has 0 unresolved dependencies Read 35917825 spots for SRR8096339/SRR8096339.sra Written 35917825 spots for SRR8096339/SRR8096339.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: 00:14:18 35917825 reads; of these: 35917825 (100.00%) were unpaired; of these: 926418 (2.58%) aligned 0 times 10028698 (27.92%) aligned exactly 1 time 24962709 (69.50%) aligned >1 times 97.42% overall alignment rate Time searching: 00:14:18 Overall time: 00:14:18 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] 18812193 / 34991407 = 0.5376 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 21:30:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.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 21:30:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:30:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:30:21: 1000000 INFO @ Sun, 21 Jun 2020 21:30:27: 2000000 INFO @ Sun, 21 Jun 2020 21:30:32: 3000000 INFO @ Sun, 21 Jun 2020 21:30:38: 4000000 INFO @ Sun, 21 Jun 2020 21:30:43: 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 21:30:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.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 21:30:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:30:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:30:50: 6000000 INFO @ Sun, 21 Jun 2020 21:30:53: 1000000 INFO @ Sun, 21 Jun 2020 21:30:57: 7000000 INFO @ Sun, 21 Jun 2020 21:31:00: 2000000 INFO @ Sun, 21 Jun 2020 21:31:04: 8000000 INFO @ Sun, 21 Jun 2020 21:31:07: 3000000 INFO @ Sun, 21 Jun 2020 21:31:11: 9000000 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 21:31:14: 4000000 INFO @ Sun, 21 Jun 2020 21:31:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.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 21:31:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:31:18: 10000000 INFO @ Sun, 21 Jun 2020 21:31:21: 5000000 INFO @ Sun, 21 Jun 2020 21:31:23: 1000000 INFO @ Sun, 21 Jun 2020 21:31:25: 11000000 INFO @ Sun, 21 Jun 2020 21:31:28: 6000000 INFO @ Sun, 21 Jun 2020 21:31:30: 2000000 INFO @ Sun, 21 Jun 2020 21:31:33: 12000000 INFO @ Sun, 21 Jun 2020 21:31:36: 7000000 INFO @ Sun, 21 Jun 2020 21:31:36: 3000000 INFO @ Sun, 21 Jun 2020 21:31:40: 13000000 INFO @ Sun, 21 Jun 2020 21:31:43: 4000000 INFO @ Sun, 21 Jun 2020 21:31:44: 8000000 INFO @ Sun, 21 Jun 2020 21:31:48: 14000000 INFO @ Sun, 21 Jun 2020 21:31:50: 5000000 INFO @ Sun, 21 Jun 2020 21:31:51: 9000000 INFO @ Sun, 21 Jun 2020 21:31:55: 15000000 INFO @ Sun, 21 Jun 2020 21:31:57: 6000000 INFO @ Sun, 21 Jun 2020 21:31:59: 10000000 INFO @ Sun, 21 Jun 2020 21:32:02: 16000000 INFO @ Sun, 21 Jun 2020 21:32:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:32:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:32:04: #1 total tags in treatment: 16179214 INFO @ Sun, 21 Jun 2020 21:32:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:04: #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 21:32:04: 7000000 INFO @ Sun, 21 Jun 2020 21:32:04: #1 tags after filtering in treatment: 16179166 INFO @ Sun, 21 Jun 2020 21:32:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:06: #2 number of paired peaks: 7440 INFO @ Sun, 21 Jun 2020 21:32:06: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:06: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:06: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:06: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:06: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 21:32:06: #2 alternative fragment length(s) may be 2,70 bps INFO @ Sun, 21 Jun 2020 21:32:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.05_model.r WARNING @ Sun, 21 Jun 2020 21:32:06: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:32:06: #2 You may need to consider one of the other alternative d(s): 2,70 WARNING @ Sun, 21 Jun 2020 21:32:06: #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 21:32:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:07: 11000000 INFO @ Sun, 21 Jun 2020 21:32:11: 8000000 INFO @ Sun, 21 Jun 2020 21:32:15: 12000000 INFO @ Sun, 21 Jun 2020 21:32:18: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:32:22: 13000000 INFO @ Sun, 21 Jun 2020 21:32:24: 10000000 INFO @ Sun, 21 Jun 2020 21:32:30: 14000000 INFO @ Sun, 21 Jun 2020 21:32:31: 11000000 INFO @ Sun, 21 Jun 2020 21:32:37: 15000000 INFO @ Sun, 21 Jun 2020 21:32:38: 12000000 INFO @ Sun, 21 Jun 2020 21:32:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:32:45: 13000000 INFO @ Sun, 21 Jun 2020 21:32:45: 16000000 INFO @ Sun, 21 Jun 2020 21:32:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:32:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:32:46: #1 total tags in treatment: 16179214 INFO @ Sun, 21 Jun 2020 21:32:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:32:47: #1 tags after filtering in treatment: 16179166 INFO @ Sun, 21 Jun 2020 21:32:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:47: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:49: #2 number of paired peaks: 7440 INFO @ Sun, 21 Jun 2020 21:32:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:49: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 21:32:49: #2 alternative fragment length(s) may be 2,70 bps INFO @ Sun, 21 Jun 2020 21:32:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.10_model.r WARNING @ Sun, 21 Jun 2020 21:32:49: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:32:49: #2 You may need to consider one of the other alternative d(s): 2,70 WARNING @ Sun, 21 Jun 2020 21:32:49: #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 21:32:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:51: 14000000 INFO @ Sun, 21 Jun 2020 21:32:57: 15000000 INFO @ Sun, 21 Jun 2020 21:32:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:32:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:32:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.05_summits.bed INFO @ Sun, 21 Jun 2020 21:32:59: Done! pass1 - making usageList (1227 chroms): 3 millis pass2 - checking and writing primary data (9543 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:33:03: 16000000 INFO @ Sun, 21 Jun 2020 21:33:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:33:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:33:04: #1 total tags in treatment: 16179214 INFO @ Sun, 21 Jun 2020 21:33:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:04: #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 21:33:04: #1 tags after filtering in treatment: 16179166 INFO @ Sun, 21 Jun 2020 21:33:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:06: #2 number of paired peaks: 7440 INFO @ Sun, 21 Jun 2020 21:33:06: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:06: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:06: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:06: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:06: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 21:33:06: #2 alternative fragment length(s) may be 2,70 bps INFO @ Sun, 21 Jun 2020 21:33:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.20_model.r WARNING @ Sun, 21 Jun 2020 21:33:06: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:33:06: #2 You may need to consider one of the other alternative d(s): 2,70 WARNING @ Sun, 21 Jun 2020 21:33:06: #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 21:33:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:33:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.10_summits.bed INFO @ Sun, 21 Jun 2020 21:33:43: Done! pass1 - making usageList (1101 chroms): 2 millis pass2 - checking and writing primary data (4664 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:33:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923189/SRX4923189.20_summits.bed INFO @ Sun, 21 Jun 2020 21:33:59: Done! pass1 - making usageList (856 chroms): 2 millis pass2 - checking and writing primary data (2677 records, 4 fields): 27 millis CompletedMACS2peakCalling