Job ID = 6626746 SRX = SRX7351012 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26890610 spots for SRR10673642/SRR10673642.sra Written 26890610 spots for SRR10673642/SRR10673642.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627032 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:21 26890610 reads; of these: 26890610 (100.00%) were unpaired; of these: 764359 (2.84%) aligned 0 times 21004414 (78.11%) aligned exactly 1 time 5121837 (19.05%) aligned >1 times 97.16% overall alignment rate Time searching: 00:10:22 Overall time: 00:10:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 6488230 / 26126251 = 0.2483 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 @ Tue, 14 Jul 2020 08:52:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.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 @ Tue, 14 Jul 2020 08:52:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:52:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:52:41: 1000000 INFO @ Tue, 14 Jul 2020 08:52:47: 2000000 INFO @ Tue, 14 Jul 2020 08:52:54: 3000000 INFO @ Tue, 14 Jul 2020 08:53:00: 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 @ Tue, 14 Jul 2020 08:53:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.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 @ Tue, 14 Jul 2020 08:53:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:53:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:53:06: 5000000 INFO @ Tue, 14 Jul 2020 08:53:14: 1000000 INFO @ Tue, 14 Jul 2020 08:53:14: 6000000 INFO @ Tue, 14 Jul 2020 08:53:22: 7000000 INFO @ Tue, 14 Jul 2020 08:53:22: 2000000 INFO @ Tue, 14 Jul 2020 08:53:29: 8000000 INFO @ Tue, 14 Jul 2020 08:53:31: 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 @ Tue, 14 Jul 2020 08:53:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.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 @ Tue, 14 Jul 2020 08:53:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:53:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:53:37: 9000000 INFO @ Tue, 14 Jul 2020 08:53:40: 4000000 INFO @ Tue, 14 Jul 2020 08:53:43: 1000000 INFO @ Tue, 14 Jul 2020 08:53:45: 10000000 INFO @ Tue, 14 Jul 2020 08:53:49: 5000000 INFO @ Tue, 14 Jul 2020 08:53:52: 2000000 INFO @ Tue, 14 Jul 2020 08:53:53: 11000000 INFO @ Tue, 14 Jul 2020 08:53:58: 6000000 INFO @ Tue, 14 Jul 2020 08:54:00: 12000000 INFO @ Tue, 14 Jul 2020 08:54:01: 3000000 INFO @ Tue, 14 Jul 2020 08:54:06: 7000000 INFO @ Tue, 14 Jul 2020 08:54:08: 13000000 INFO @ Tue, 14 Jul 2020 08:54:10: 4000000 INFO @ Tue, 14 Jul 2020 08:54:15: 8000000 INFO @ Tue, 14 Jul 2020 08:54:16: 14000000 INFO @ Tue, 14 Jul 2020 08:54:19: 5000000 INFO @ Tue, 14 Jul 2020 08:54:24: 15000000 INFO @ Tue, 14 Jul 2020 08:54:24: 9000000 INFO @ Tue, 14 Jul 2020 08:54:28: 6000000 INFO @ Tue, 14 Jul 2020 08:54:32: 16000000 INFO @ Tue, 14 Jul 2020 08:54:33: 10000000 INFO @ Tue, 14 Jul 2020 08:54:37: 7000000 INFO @ Tue, 14 Jul 2020 08:54:40: 17000000 INFO @ Tue, 14 Jul 2020 08:54:41: 11000000 INFO @ Tue, 14 Jul 2020 08:54:45: 8000000 INFO @ Tue, 14 Jul 2020 08:54:48: 18000000 INFO @ Tue, 14 Jul 2020 08:54:50: 12000000 INFO @ Tue, 14 Jul 2020 08:54:54: 9000000 INFO @ Tue, 14 Jul 2020 08:54:56: 19000000 INFO @ Tue, 14 Jul 2020 08:54:58: 13000000 INFO @ Tue, 14 Jul 2020 08:55:00: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:55:00: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:55:00: #1 total tags in treatment: 19638021 INFO @ Tue, 14 Jul 2020 08:55:00: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:55:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:55:01: #1 tags after filtering in treatment: 19638021 INFO @ Tue, 14 Jul 2020 08:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:55:01: #1 finished! INFO @ Tue, 14 Jul 2020 08:55:01: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:55:03: #2 number of paired peaks: 5849 INFO @ Tue, 14 Jul 2020 08:55:03: start model_add_line... INFO @ Tue, 14 Jul 2020 08:55:03: 10000000 INFO @ Tue, 14 Jul 2020 08:55:03: start X-correlation... INFO @ Tue, 14 Jul 2020 08:55:03: end of X-cor INFO @ Tue, 14 Jul 2020 08:55:03: #2 finished! INFO @ Tue, 14 Jul 2020 08:55:03: #2 predicted fragment length is 129 bps INFO @ Tue, 14 Jul 2020 08:55:03: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 14 Jul 2020 08:55:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.05_model.r WARNING @ Tue, 14 Jul 2020 08:55:03: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:55:03: #2 You may need to consider one of the other alternative d(s): 4,129 WARNING @ Tue, 14 Jul 2020 08:55:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:55:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:55:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:55:07: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:55:11: 11000000 INFO @ Tue, 14 Jul 2020 08:55:15: 15000000 INFO @ Tue, 14 Jul 2020 08:55:19: 12000000 INFO @ Tue, 14 Jul 2020 08:55:23: 16000000 INFO @ Tue, 14 Jul 2020 08:55:28: 13000000 INFO @ Tue, 14 Jul 2020 08:55:32: 17000000 INFO @ Tue, 14 Jul 2020 08:55:36: 14000000 INFO @ Tue, 14 Jul 2020 08:55:40: 18000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:55:44: 15000000 INFO @ Tue, 14 Jul 2020 08:55:48: 19000000 INFO @ Tue, 14 Jul 2020 08:55:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:55:53: 16000000 INFO @ Tue, 14 Jul 2020 08:55:53: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:55:53: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:55:53: #1 total tags in treatment: 19638021 INFO @ Tue, 14 Jul 2020 08:55:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:55:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:55:54: #1 tags after filtering in treatment: 19638021 INFO @ Tue, 14 Jul 2020 08:55:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:55:54: #1 finished! INFO @ Tue, 14 Jul 2020 08:55:54: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:55:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:55:55: #2 number of paired peaks: 5849 INFO @ Tue, 14 Jul 2020 08:55:55: start model_add_line... INFO @ Tue, 14 Jul 2020 08:55:56: start X-correlation... INFO @ Tue, 14 Jul 2020 08:55:56: end of X-cor INFO @ Tue, 14 Jul 2020 08:55:56: #2 finished! INFO @ Tue, 14 Jul 2020 08:55:56: #2 predicted fragment length is 129 bps INFO @ Tue, 14 Jul 2020 08:55:56: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 14 Jul 2020 08:55:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.10_model.r WARNING @ Tue, 14 Jul 2020 08:55:56: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:55:56: #2 You may need to consider one of the other alternative d(s): 4,129 WARNING @ Tue, 14 Jul 2020 08:55:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:55:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:55:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:56:00: 17000000 INFO @ Tue, 14 Jul 2020 08:56:08: 18000000 INFO @ Tue, 14 Jul 2020 08:56:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:56:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:56:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.05_summits.bed INFO @ Tue, 14 Jul 2020 08:56:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14663 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:56:15: 19000000 INFO @ Tue, 14 Jul 2020 08:56:20: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:56:20: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:56:20: #1 total tags in treatment: 19638021 INFO @ Tue, 14 Jul 2020 08:56:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:56:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:56:20: #1 tags after filtering in treatment: 19638021 INFO @ Tue, 14 Jul 2020 08:56:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:56:20: #1 finished! INFO @ Tue, 14 Jul 2020 08:56:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:56:22: #2 number of paired peaks: 5849 INFO @ Tue, 14 Jul 2020 08:56:22: start model_add_line... INFO @ Tue, 14 Jul 2020 08:56:22: start X-correlation... INFO @ Tue, 14 Jul 2020 08:56:22: end of X-cor INFO @ Tue, 14 Jul 2020 08:56:22: #2 finished! INFO @ Tue, 14 Jul 2020 08:56:22: #2 predicted fragment length is 129 bps INFO @ Tue, 14 Jul 2020 08:56:22: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 14 Jul 2020 08:56:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.20_model.r WARNING @ Tue, 14 Jul 2020 08:56:22: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:56:22: #2 You may need to consider one of the other alternative d(s): 4,129 WARNING @ Tue, 14 Jul 2020 08:56:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:56:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:56:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:57:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:57:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:57:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.10_summits.bed INFO @ Tue, 14 Jul 2020 08:57:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11292 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:57:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:57:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:57:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:57:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351012/SRX7351012.20_summits.bed INFO @ Tue, 14 Jul 2020 08:57:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7090 records, 4 fields): 8 millis CompletedMACS2peakCalling