Job ID = 6626830 SRX = SRX7351001 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: 00:10:30 27964107 reads; of these: 27964107 (100.00%) were unpaired; of these: 919619 (3.29%) aligned 0 times 18850506 (67.41%) aligned exactly 1 time 8193982 (29.30%) aligned >1 times 96.71% overall alignment rate Time searching: 00:10:30 Overall time: 00:10:30 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] 5126497 / 27044488 = 0.1896 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 09:08:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.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 09:08:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:08:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:09:02: 1000000 INFO @ Tue, 14 Jul 2020 09:09:08: 2000000 INFO @ Tue, 14 Jul 2020 09:09:13: 3000000 INFO @ Tue, 14 Jul 2020 09:09:19: 4000000 INFO @ Tue, 14 Jul 2020 09:09:24: 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 09:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.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 09:09:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:09:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:09:30: 6000000 INFO @ Tue, 14 Jul 2020 09:09:32: 1000000 INFO @ Tue, 14 Jul 2020 09:09:36: 7000000 INFO @ Tue, 14 Jul 2020 09:09:38: 2000000 INFO @ Tue, 14 Jul 2020 09:09:41: 8000000 INFO @ Tue, 14 Jul 2020 09:09:44: 3000000 INFO @ Tue, 14 Jul 2020 09:09:47: 9000000 INFO @ Tue, 14 Jul 2020 09:09:50: 4000000 INFO @ Tue, 14 Jul 2020 09:09:53: 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 @ Tue, 14 Jul 2020 09:09:55: 5000000 INFO @ Tue, 14 Jul 2020 09:09:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.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 09:09:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:09:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:09:59: 11000000 INFO @ Tue, 14 Jul 2020 09:10:01: 6000000 INFO @ Tue, 14 Jul 2020 09:10:02: 1000000 INFO @ Tue, 14 Jul 2020 09:10:04: 12000000 INFO @ Tue, 14 Jul 2020 09:10:07: 7000000 INFO @ Tue, 14 Jul 2020 09:10:08: 2000000 INFO @ Tue, 14 Jul 2020 09:10:10: 13000000 INFO @ Tue, 14 Jul 2020 09:10:13: 8000000 INFO @ Tue, 14 Jul 2020 09:10:14: 3000000 INFO @ Tue, 14 Jul 2020 09:10:16: 14000000 INFO @ Tue, 14 Jul 2020 09:10:18: 9000000 INFO @ Tue, 14 Jul 2020 09:10:20: 4000000 INFO @ Tue, 14 Jul 2020 09:10:22: 15000000 INFO @ Tue, 14 Jul 2020 09:10:24: 10000000 INFO @ Tue, 14 Jul 2020 09:10:26: 5000000 INFO @ Tue, 14 Jul 2020 09:10:27: 16000000 INFO @ Tue, 14 Jul 2020 09:10:30: 11000000 INFO @ Tue, 14 Jul 2020 09:10:32: 6000000 INFO @ Tue, 14 Jul 2020 09:10:33: 17000000 INFO @ Tue, 14 Jul 2020 09:10:36: 12000000 INFO @ Tue, 14 Jul 2020 09:10:37: 7000000 INFO @ Tue, 14 Jul 2020 09:10:39: 18000000 INFO @ Tue, 14 Jul 2020 09:10:41: 13000000 INFO @ Tue, 14 Jul 2020 09:10:43: 8000000 INFO @ Tue, 14 Jul 2020 09:10:45: 19000000 INFO @ Tue, 14 Jul 2020 09:10:47: 14000000 INFO @ Tue, 14 Jul 2020 09:10:49: 9000000 INFO @ Tue, 14 Jul 2020 09:10:50: 20000000 INFO @ Tue, 14 Jul 2020 09:10:53: 15000000 INFO @ Tue, 14 Jul 2020 09:10:55: 10000000 INFO @ Tue, 14 Jul 2020 09:10:56: 21000000 INFO @ Tue, 14 Jul 2020 09:10:58: 16000000 INFO @ Tue, 14 Jul 2020 09:11:00: 11000000 INFO @ Tue, 14 Jul 2020 09:11:01: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:11:01: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:11:01: #1 total tags in treatment: 21917991 INFO @ Tue, 14 Jul 2020 09:11:01: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:11:01: #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 09:11:02: #1 tags after filtering in treatment: 21917884 INFO @ Tue, 14 Jul 2020 09:11:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:11:02: #1 finished! INFO @ Tue, 14 Jul 2020 09:11:02: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:11:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:11:03: #2 number of paired peaks: 1082 INFO @ Tue, 14 Jul 2020 09:11:03: start model_add_line... INFO @ Tue, 14 Jul 2020 09:11:04: start X-correlation... INFO @ Tue, 14 Jul 2020 09:11:04: end of X-cor INFO @ Tue, 14 Jul 2020 09:11:04: #2 finished! INFO @ Tue, 14 Jul 2020 09:11:04: #2 predicted fragment length is 69 bps INFO @ Tue, 14 Jul 2020 09:11:04: #2 alternative fragment length(s) may be 2,69,586,589 bps INFO @ Tue, 14 Jul 2020 09:11:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.05_model.r WARNING @ Tue, 14 Jul 2020 09:11:04: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:11:04: #2 You may need to consider one of the other alternative d(s): 2,69,586,589 WARNING @ Tue, 14 Jul 2020 09:11:04: #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 09:11:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:11:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:11:04: 17000000 INFO @ Tue, 14 Jul 2020 09:11:06: 12000000 INFO @ Tue, 14 Jul 2020 09:11:10: 18000000 INFO @ Tue, 14 Jul 2020 09:11:12: 13000000 INFO @ Tue, 14 Jul 2020 09:11:16: 19000000 INFO @ Tue, 14 Jul 2020 09:11:17: 14000000 INFO @ Tue, 14 Jul 2020 09:11:21: 20000000 INFO @ Tue, 14 Jul 2020 09:11:23: 15000000 INFO @ Tue, 14 Jul 2020 09:11:27: 21000000 INFO @ Tue, 14 Jul 2020 09:11:29: 16000000 INFO @ Tue, 14 Jul 2020 09:11:32: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:11:32: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:11:32: #1 total tags in treatment: 21917991 INFO @ Tue, 14 Jul 2020 09:11:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:11:32: #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 09:11:33: #1 tags after filtering in treatment: 21917884 INFO @ Tue, 14 Jul 2020 09:11:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:11:33: #1 finished! INFO @ Tue, 14 Jul 2020 09:11:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:11:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:11:34: 17000000 INFO @ Tue, 14 Jul 2020 09:11:34: #2 number of paired peaks: 1082 INFO @ Tue, 14 Jul 2020 09:11:34: start model_add_line... INFO @ Tue, 14 Jul 2020 09:11:35: start X-correlation... INFO @ Tue, 14 Jul 2020 09:11:35: end of X-cor INFO @ Tue, 14 Jul 2020 09:11:35: #2 finished! INFO @ Tue, 14 Jul 2020 09:11:35: #2 predicted fragment length is 69 bps INFO @ Tue, 14 Jul 2020 09:11:35: #2 alternative fragment length(s) may be 2,69,586,589 bps INFO @ Tue, 14 Jul 2020 09:11:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.10_model.r WARNING @ Tue, 14 Jul 2020 09:11:35: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:11:35: #2 You may need to consider one of the other alternative d(s): 2,69,586,589 WARNING @ Tue, 14 Jul 2020 09:11:35: #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 09:11:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:11:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:11:40: 18000000 INFO @ Tue, 14 Jul 2020 09:11:43: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:11:45: 19000000 INFO @ Tue, 14 Jul 2020 09:11:51: 20000000 INFO @ Tue, 14 Jul 2020 09:11:56: 21000000 INFO @ Tue, 14 Jul 2020 09:12:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:12:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:12:01: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:12:01: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:12:01: #1 total tags in treatment: 21917991 INFO @ Tue, 14 Jul 2020 09:12:01: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:12:01: #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 09:12:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.05_summits.bed INFO @ Tue, 14 Jul 2020 09:12:01: Done! pass1 - making usageList (615 chroms): 2 millis pass2 - checking and writing primary data (3303 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:12:02: #1 tags after filtering in treatment: 21917884 INFO @ Tue, 14 Jul 2020 09:12:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:12:02: #1 finished! INFO @ Tue, 14 Jul 2020 09:12:02: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:12:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:12:03: #2 number of paired peaks: 1082 INFO @ Tue, 14 Jul 2020 09:12:03: start model_add_line... INFO @ Tue, 14 Jul 2020 09:12:04: start X-correlation... INFO @ Tue, 14 Jul 2020 09:12:04: end of X-cor INFO @ Tue, 14 Jul 2020 09:12:04: #2 finished! INFO @ Tue, 14 Jul 2020 09:12:04: #2 predicted fragment length is 69 bps INFO @ Tue, 14 Jul 2020 09:12:04: #2 alternative fragment length(s) may be 2,69,586,589 bps INFO @ Tue, 14 Jul 2020 09:12:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.20_model.r WARNING @ Tue, 14 Jul 2020 09:12:04: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:12:04: #2 You may need to consider one of the other alternative d(s): 2,69,586,589 WARNING @ Tue, 14 Jul 2020 09:12:04: #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 09:12:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:12:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:12:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:12:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:12:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.10_summits.bed INFO @ Tue, 14 Jul 2020 09:12:32: Done! pass1 - making usageList (550 chroms): 2 millis pass2 - checking and writing primary data (2013 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:12:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:13:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:13:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:13:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351001/SRX7351001.20_summits.bed INFO @ Tue, 14 Jul 2020 09:13:00: Done! pass1 - making usageList (412 chroms): 1 millis pass2 - checking and writing primary data (1005 records, 4 fields): 13 millis CompletedMACS2peakCalling