Job ID = 6457937 SRX = SRX4923183 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:08:40 prefetch.2.10.7: 1) Downloading 'SRR8096333'... 2020-06-21T12:08:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:10:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:10:16 prefetch.2.10.7: 'SRR8096333' is valid 2020-06-21T12:10:16 prefetch.2.10.7: 1) 'SRR8096333' was downloaded successfully 2020-06-21T12:10:16 prefetch.2.10.7: 'SRR8096333' has 0 unresolved dependencies Read 20403846 spots for SRR8096333/SRR8096333.sra Written 20403846 spots for SRR8096333/SRR8096333.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: 00:07:04 20403846 reads; of these: 20403846 (100.00%) were unpaired; of these: 583691 (2.86%) aligned 0 times 5869972 (28.77%) aligned exactly 1 time 13950183 (68.37%) aligned >1 times 97.14% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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 12 files... [bam_rmdupse_core] 8438470 / 19820155 = 0.4258 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 21:21:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.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 21:21:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:21:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:21:54: 1000000 INFO @ Sun, 21 Jun 2020 21:21:59: 2000000 INFO @ Sun, 21 Jun 2020 21:22:05: 3000000 INFO @ Sun, 21 Jun 2020 21:22:10: 4000000 INFO @ Sun, 21 Jun 2020 21:22:16: 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 21:22:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.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 21:22:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:22:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:22:22: 6000000 INFO @ Sun, 21 Jun 2020 21:22:25: 1000000 INFO @ Sun, 21 Jun 2020 21:22:28: 7000000 INFO @ Sun, 21 Jun 2020 21:22:31: 2000000 INFO @ Sun, 21 Jun 2020 21:22:34: 8000000 INFO @ Sun, 21 Jun 2020 21:22:37: 3000000 INFO @ Sun, 21 Jun 2020 21:22:40: 9000000 INFO @ Sun, 21 Jun 2020 21:22:43: 4000000 INFO @ Sun, 21 Jun 2020 21:22:46: 10000000 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 21:22:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.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 21:22:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:22:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:22:49: 5000000 INFO @ Sun, 21 Jun 2020 21:22:52: 11000000 INFO @ Sun, 21 Jun 2020 21:22:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:22:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:22:55: #1 total tags in treatment: 11381685 INFO @ Sun, 21 Jun 2020 21:22:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:55: #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 21:22:55: 1000000 INFO @ Sun, 21 Jun 2020 21:22:55: #1 tags after filtering in treatment: 11381624 INFO @ Sun, 21 Jun 2020 21:22:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:55: 6000000 INFO @ Sun, 21 Jun 2020 21:22:56: #2 number of paired peaks: 7150 INFO @ Sun, 21 Jun 2020 21:22:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:57: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 21:22:57: #2 alternative fragment length(s) may be 3,100 bps INFO @ Sun, 21 Jun 2020 21:22:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.05_model.r WARNING @ Sun, 21 Jun 2020 21:22:57: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:22:57: #2 You may need to consider one of the other alternative d(s): 3,100 WARNING @ Sun, 21 Jun 2020 21:22:57: #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 21:22:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:23:01: 2000000 INFO @ Sun, 21 Jun 2020 21:23:01: 7000000 INFO @ Sun, 21 Jun 2020 21:23:07: 3000000 INFO @ Sun, 21 Jun 2020 21:23:08: 8000000 INFO @ Sun, 21 Jun 2020 21:23:13: 4000000 INFO @ Sun, 21 Jun 2020 21:23:14: 9000000 INFO @ Sun, 21 Jun 2020 21:23:19: 5000000 INFO @ Sun, 21 Jun 2020 21:23:20: 10000000 INFO @ Sun, 21 Jun 2020 21:23:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:25: 6000000 INFO @ Sun, 21 Jun 2020 21:23:27: 11000000 INFO @ Sun, 21 Jun 2020 21:23:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:23:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:23:29: #1 total tags in treatment: 11381685 INFO @ Sun, 21 Jun 2020 21:23:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:23:29: #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 21:23:30: #1 tags after filtering in treatment: 11381624 INFO @ Sun, 21 Jun 2020 21:23:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:23:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:23:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:23:31: #2 number of paired peaks: 7150 INFO @ Sun, 21 Jun 2020 21:23:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:23:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:23:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:23:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:23:31: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 21:23:31: #2 alternative fragment length(s) may be 3,100 bps INFO @ Sun, 21 Jun 2020 21:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.10_model.r WARNING @ Sun, 21 Jun 2020 21:23:31: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:23:31: #2 You may need to consider one of the other alternative d(s): 3,100 WARNING @ Sun, 21 Jun 2020 21:23:31: #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 21:23:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:23:31: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:23:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.05_summits.bed INFO @ Sun, 21 Jun 2020 21:23:36: Done! pass1 - making usageList (1072 chroms): 2 millis pass2 - checking and writing primary data (7741 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:23:37: 8000000 INFO @ Sun, 21 Jun 2020 21:23:43: 9000000 INFO @ Sun, 21 Jun 2020 21:23:49: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:23:55: 11000000 INFO @ Sun, 21 Jun 2020 21:23:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:23:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:23:57: #1 total tags in treatment: 11381685 INFO @ Sun, 21 Jun 2020 21:23:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:23:57: #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 21:23:57: #1 tags after filtering in treatment: 11381624 INFO @ Sun, 21 Jun 2020 21:23:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:23:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:23:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:23:58: #2 number of paired peaks: 7150 INFO @ Sun, 21 Jun 2020 21:23:58: start model_add_line... INFO @ Sun, 21 Jun 2020 21:23:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:23:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:23:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:23:59: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 21:23:59: #2 alternative fragment length(s) may be 3,100 bps INFO @ Sun, 21 Jun 2020 21:23:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.20_model.r WARNING @ Sun, 21 Jun 2020 21:23:59: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:23:59: #2 You may need to consider one of the other alternative d(s): 3,100 WARNING @ Sun, 21 Jun 2020 21:23:59: #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 21:23:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:23:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:24:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:24:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:24:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.10_summits.bed INFO @ Sun, 21 Jun 2020 21:24:12: Done! pass1 - making usageList (951 chroms): 2 millis pass2 - checking and writing primary data (3988 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:24:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:24:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:24:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:24:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923183/SRX4923183.20_summits.bed INFO @ Sun, 21 Jun 2020 21:24:38: Done! pass1 - making usageList (766 chroms): 2 millis pass2 - checking and writing primary data (2026 records, 4 fields): 21 millis CompletedMACS2peakCalling