Job ID = 6626977 SRX = SRX7351011 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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 22252888 reads; of these: 22252888 (100.00%) were unpaired; of these: 660401 (2.97%) aligned 0 times 17795552 (79.97%) aligned exactly 1 time 3796935 (17.06%) aligned >1 times 97.03% 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] 5903589 / 21592487 = 0.2734 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 09:19:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.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 09:19:45: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:19:45: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:19:51: 1000000 INFO @ Tue, 14 Jul 2020 09:19:56: 2000000 INFO @ Tue, 14 Jul 2020 09:20:01: 3000000 INFO @ Tue, 14 Jul 2020 09:20:06: 4000000 INFO @ Tue, 14 Jul 2020 09:20:11: 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 @ Tue, 14 Jul 2020 09:20:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.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 09:20:15: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:20:15: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:20:16: 6000000 INFO @ Tue, 14 Jul 2020 09:20:21: 7000000 INFO @ Tue, 14 Jul 2020 09:20:22: 1000000 INFO @ Tue, 14 Jul 2020 09:20:27: 8000000 INFO @ Tue, 14 Jul 2020 09:20:28: 2000000 INFO @ Tue, 14 Jul 2020 09:20:32: 9000000 INFO @ Tue, 14 Jul 2020 09:20:34: 3000000 INFO @ Tue, 14 Jul 2020 09:20:37: 10000000 INFO @ Tue, 14 Jul 2020 09:20:40: 4000000 INFO @ Tue, 14 Jul 2020 09:20:43: 11000000 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 09:20:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.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 09:20:46: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:20:46: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:20:47: 5000000 INFO @ Tue, 14 Jul 2020 09:20:48: 12000000 INFO @ Tue, 14 Jul 2020 09:20:52: 1000000 INFO @ Tue, 14 Jul 2020 09:20:53: 6000000 INFO @ Tue, 14 Jul 2020 09:20:53: 13000000 INFO @ Tue, 14 Jul 2020 09:20:58: 2000000 INFO @ Tue, 14 Jul 2020 09:20:59: 14000000 INFO @ Tue, 14 Jul 2020 09:20:59: 7000000 INFO @ Tue, 14 Jul 2020 09:21:05: 15000000 INFO @ Tue, 14 Jul 2020 09:21:05: 3000000 INFO @ Tue, 14 Jul 2020 09:21:06: 8000000 INFO @ Tue, 14 Jul 2020 09:21:09: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:21:09: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:21:09: #1 total tags in treatment: 15688898 INFO @ Tue, 14 Jul 2020 09:21:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:21:09: #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 09:21:09: #1 tags after filtering in treatment: 15688659 INFO @ Tue, 14 Jul 2020 09:21:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:21:09: #1 finished! INFO @ Tue, 14 Jul 2020 09:21:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:21:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:21:11: #2 number of paired peaks: 8685 INFO @ Tue, 14 Jul 2020 09:21:11: start model_add_line... INFO @ Tue, 14 Jul 2020 09:21:11: 4000000 INFO @ Tue, 14 Jul 2020 09:21:11: start X-correlation... INFO @ Tue, 14 Jul 2020 09:21:11: end of X-cor INFO @ Tue, 14 Jul 2020 09:21:11: #2 finished! INFO @ Tue, 14 Jul 2020 09:21:11: #2 predicted fragment length is 149 bps INFO @ Tue, 14 Jul 2020 09:21:11: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 14 Jul 2020 09:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.05_model.r WARNING @ Tue, 14 Jul 2020 09:21:11: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:21:11: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Tue, 14 Jul 2020 09:21:11: #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 09:21:11: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:21:12: 9000000 INFO @ Tue, 14 Jul 2020 09:21:17: 5000000 INFO @ Tue, 14 Jul 2020 09:21:18: 10000000 INFO @ Tue, 14 Jul 2020 09:21:24: 6000000 INFO @ Tue, 14 Jul 2020 09:21:25: 11000000 INFO @ Tue, 14 Jul 2020 09:21:30: 7000000 INFO @ Tue, 14 Jul 2020 09:21:31: 12000000 INFO @ Tue, 14 Jul 2020 09:21:36: 8000000 INFO @ Tue, 14 Jul 2020 09:21:37: 13000000 INFO @ Tue, 14 Jul 2020 09:21:43: 9000000 INFO @ Tue, 14 Jul 2020 09:21:44: 14000000 INFO @ Tue, 14 Jul 2020 09:21:49: 10000000 INFO @ Tue, 14 Jul 2020 09:21:50: 15000000 INFO @ Tue, 14 Jul 2020 09:21:55: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:21:55: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:21:55: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:21:55: #1 total tags in treatment: 15688898 INFO @ Tue, 14 Jul 2020 09:21:55: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:21:55: #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 09:21:55: 11000000 INFO @ Tue, 14 Jul 2020 09:21:56: #1 tags after filtering in treatment: 15688659 INFO @ Tue, 14 Jul 2020 09:21:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:21:56: #1 finished! INFO @ Tue, 14 Jul 2020 09:21:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:21:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:21:57: #2 number of paired peaks: 8685 INFO @ Tue, 14 Jul 2020 09:21:57: start model_add_line... INFO @ Tue, 14 Jul 2020 09:21:58: start X-correlation... INFO @ Tue, 14 Jul 2020 09:21:58: end of X-cor INFO @ Tue, 14 Jul 2020 09:21:58: #2 finished! INFO @ Tue, 14 Jul 2020 09:21:58: #2 predicted fragment length is 149 bps INFO @ Tue, 14 Jul 2020 09:21:58: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 14 Jul 2020 09:21:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.10_model.r WARNING @ Tue, 14 Jul 2020 09:21:58: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:21:58: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Tue, 14 Jul 2020 09:21:58: #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 09:21:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:21:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:22:02: 12000000 INFO @ Tue, 14 Jul 2020 09:22:08: 13000000 INFO @ Tue, 14 Jul 2020 09:22:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:22:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:22:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.05_summits.bed INFO @ Tue, 14 Jul 2020 09:22:14: Done! INFO @ Tue, 14 Jul 2020 09:22:14: 14000000 pass1 - making usageList (199 chroms): 2 millis pass2 - checking and writing primary data (13553 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:22:21: 15000000 INFO @ Tue, 14 Jul 2020 09:22:25: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:22:25: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:22:25: #1 total tags in treatment: 15688898 INFO @ Tue, 14 Jul 2020 09:22:25: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:22:25: #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 09:22:25: #1 tags after filtering in treatment: 15688659 INFO @ Tue, 14 Jul 2020 09:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:22:25: #1 finished! INFO @ Tue, 14 Jul 2020 09:22:25: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:22:27: #2 number of paired peaks: 8685 INFO @ Tue, 14 Jul 2020 09:22:27: start model_add_line... INFO @ Tue, 14 Jul 2020 09:22:27: start X-correlation... INFO @ Tue, 14 Jul 2020 09:22:27: end of X-cor INFO @ Tue, 14 Jul 2020 09:22:27: #2 finished! INFO @ Tue, 14 Jul 2020 09:22:27: #2 predicted fragment length is 149 bps INFO @ Tue, 14 Jul 2020 09:22:27: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 14 Jul 2020 09:22:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.20_model.r WARNING @ Tue, 14 Jul 2020 09:22:27: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:22:27: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Tue, 14 Jul 2020 09:22:27: #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 09:22:27: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:22:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:22:38: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.10_summits.bed INFO @ Tue, 14 Jul 2020 09:22:55: Done! pass1 - making usageList (178 chroms): 2 millis pass2 - checking and writing primary data (11175 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:23:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:23:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:23:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:23:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351011/SRX7351011.20_summits.bed INFO @ Tue, 14 Jul 2020 09:23:25: Done! pass1 - making usageList (142 chroms): 2 millis pass2 - checking and writing primary data (7708 records, 4 fields): 11 millis CompletedMACS2peakCalling