Job ID = 6529315 SRX = SRX159171 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: 00:06:46 29495696 reads; of these: 29495696 (100.00%) were unpaired; of these: 3129081 (10.61%) aligned 0 times 18080146 (61.30%) aligned exactly 1 time 8286469 (28.09%) aligned >1 times 89.39% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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 8 files... [bam_rmdupse_core] 3829749 / 26366615 = 0.1452 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, 30 Jun 2020 01:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.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, 30 Jun 2020 01:56:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:56:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:02: 1000000 INFO @ Tue, 30 Jun 2020 01:57:08: 2000000 INFO @ Tue, 30 Jun 2020 01:57:14: 3000000 INFO @ Tue, 30 Jun 2020 01:57:20: 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, 30 Jun 2020 01:57:26: 5000000 INFO @ Tue, 30 Jun 2020 01:57:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.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, 30 Jun 2020 01:57:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:32: 6000000 INFO @ Tue, 30 Jun 2020 01:57:32: 1000000 INFO @ Tue, 30 Jun 2020 01:57:38: 7000000 INFO @ Tue, 30 Jun 2020 01:57:39: 2000000 INFO @ Tue, 30 Jun 2020 01:57:43: 8000000 INFO @ Tue, 30 Jun 2020 01:57:45: 3000000 INFO @ Tue, 30 Jun 2020 01:57:49: 9000000 INFO @ Tue, 30 Jun 2020 01:57:51: 4000000 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, 30 Jun 2020 01:57:55: 10000000 INFO @ Tue, 30 Jun 2020 01:57:57: 5000000 INFO @ Tue, 30 Jun 2020 01:57:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.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, 30 Jun 2020 01:57:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:01: 11000000 INFO @ Tue, 30 Jun 2020 01:58:03: 6000000 INFO @ Tue, 30 Jun 2020 01:58:04: 1000000 INFO @ Tue, 30 Jun 2020 01:58:08: 12000000 INFO @ Tue, 30 Jun 2020 01:58:09: 7000000 INFO @ Tue, 30 Jun 2020 01:58:10: 2000000 INFO @ Tue, 30 Jun 2020 01:58:14: 13000000 INFO @ Tue, 30 Jun 2020 01:58:14: 8000000 INFO @ Tue, 30 Jun 2020 01:58:16: 3000000 INFO @ Tue, 30 Jun 2020 01:58:20: 14000000 INFO @ Tue, 30 Jun 2020 01:58:20: 9000000 INFO @ Tue, 30 Jun 2020 01:58:22: 4000000 INFO @ Tue, 30 Jun 2020 01:58:26: 15000000 INFO @ Tue, 30 Jun 2020 01:58:26: 10000000 INFO @ Tue, 30 Jun 2020 01:58:28: 5000000 INFO @ Tue, 30 Jun 2020 01:58:32: 16000000 INFO @ Tue, 30 Jun 2020 01:58:32: 11000000 INFO @ Tue, 30 Jun 2020 01:58:34: 6000000 INFO @ Tue, 30 Jun 2020 01:58:38: 17000000 INFO @ Tue, 30 Jun 2020 01:58:38: 12000000 INFO @ Tue, 30 Jun 2020 01:58:40: 7000000 INFO @ Tue, 30 Jun 2020 01:58:44: 18000000 INFO @ Tue, 30 Jun 2020 01:58:44: 13000000 INFO @ Tue, 30 Jun 2020 01:58:46: 8000000 INFO @ Tue, 30 Jun 2020 01:58:50: 14000000 INFO @ Tue, 30 Jun 2020 01:58:51: 19000000 INFO @ Tue, 30 Jun 2020 01:58:52: 9000000 INFO @ Tue, 30 Jun 2020 01:58:56: 15000000 INFO @ Tue, 30 Jun 2020 01:58:57: 20000000 INFO @ Tue, 30 Jun 2020 01:58:59: 10000000 INFO @ Tue, 30 Jun 2020 01:59:02: 16000000 INFO @ Tue, 30 Jun 2020 01:59:03: 21000000 INFO @ Tue, 30 Jun 2020 01:59:05: 11000000 INFO @ Tue, 30 Jun 2020 01:59:09: 17000000 INFO @ Tue, 30 Jun 2020 01:59:09: 22000000 INFO @ Tue, 30 Jun 2020 01:59:10: 12000000 INFO @ Tue, 30 Jun 2020 01:59:13: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:59:13: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:59:13: #1 total tags in treatment: 22536866 INFO @ Tue, 30 Jun 2020 01:59:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:59:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:59:13: #1 tags after filtering in treatment: 22536821 INFO @ Tue, 30 Jun 2020 01:59:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:59:13: #1 finished! INFO @ Tue, 30 Jun 2020 01:59:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:59:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:59:15: 18000000 INFO @ Tue, 30 Jun 2020 01:59:15: #2 number of paired peaks: 836 WARNING @ Tue, 30 Jun 2020 01:59:15: Fewer paired peaks (836) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 836 pairs to build model! INFO @ Tue, 30 Jun 2020 01:59:15: start model_add_line... INFO @ Tue, 30 Jun 2020 01:59:15: start X-correlation... INFO @ Tue, 30 Jun 2020 01:59:15: end of X-cor INFO @ Tue, 30 Jun 2020 01:59:15: #2 finished! INFO @ Tue, 30 Jun 2020 01:59:15: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 01:59:15: #2 alternative fragment length(s) may be 1,36 bps INFO @ Tue, 30 Jun 2020 01:59:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.05_model.r WARNING @ Tue, 30 Jun 2020 01:59:15: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:59:15: #2 You may need to consider one of the other alternative d(s): 1,36 WARNING @ Tue, 30 Jun 2020 01:59:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:59:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:59:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:59:16: 13000000 INFO @ Tue, 30 Jun 2020 01:59:21: 19000000 INFO @ Tue, 30 Jun 2020 01:59:23: 14000000 INFO @ Tue, 30 Jun 2020 01:59:27: 20000000 INFO @ Tue, 30 Jun 2020 01:59:29: 15000000 INFO @ Tue, 30 Jun 2020 01:59:33: 21000000 INFO @ Tue, 30 Jun 2020 01:59:35: 16000000 INFO @ Tue, 30 Jun 2020 01:59:39: 22000000 INFO @ Tue, 30 Jun 2020 01:59:41: 17000000 INFO @ Tue, 30 Jun 2020 01:59:43: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:59:43: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:59:43: #1 total tags in treatment: 22536866 INFO @ Tue, 30 Jun 2020 01:59:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:59:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:59:44: #1 tags after filtering in treatment: 22536821 INFO @ Tue, 30 Jun 2020 01:59:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:59:44: #1 finished! INFO @ Tue, 30 Jun 2020 01:59:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:59:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:59:45: #2 number of paired peaks: 836 WARNING @ Tue, 30 Jun 2020 01:59:45: Fewer paired peaks (836) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 836 pairs to build model! INFO @ Tue, 30 Jun 2020 01:59:45: start model_add_line... INFO @ Tue, 30 Jun 2020 01:59:45: start X-correlation... INFO @ Tue, 30 Jun 2020 01:59:45: end of X-cor INFO @ Tue, 30 Jun 2020 01:59:45: #2 finished! INFO @ Tue, 30 Jun 2020 01:59:45: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 01:59:45: #2 alternative fragment length(s) may be 1,36 bps INFO @ Tue, 30 Jun 2020 01:59:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.10_model.r WARNING @ Tue, 30 Jun 2020 01:59:45: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:59:45: #2 You may need to consider one of the other alternative d(s): 1,36 WARNING @ Tue, 30 Jun 2020 01:59:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:59:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:59:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:59:47: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:59:53: 19000000 INFO @ Tue, 30 Jun 2020 01:59:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:59:59: 20000000 INFO @ Tue, 30 Jun 2020 02:00:05: 21000000 INFO @ Tue, 30 Jun 2020 02:00:11: 22000000 INFO @ Tue, 30 Jun 2020 02:00:15: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:00:15: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:00:15: #1 total tags in treatment: 22536866 INFO @ Tue, 30 Jun 2020 02:00:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:00:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:00:15: #1 tags after filtering in treatment: 22536821 INFO @ Tue, 30 Jun 2020 02:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:00:15: #1 finished! INFO @ Tue, 30 Jun 2020 02:00:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:00:17: #2 number of paired peaks: 836 WARNING @ Tue, 30 Jun 2020 02:00:17: Fewer paired peaks (836) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 836 pairs to build model! INFO @ Tue, 30 Jun 2020 02:00:17: start model_add_line... INFO @ Tue, 30 Jun 2020 02:00:17: start X-correlation... INFO @ Tue, 30 Jun 2020 02:00:17: end of X-cor INFO @ Tue, 30 Jun 2020 02:00:17: #2 finished! INFO @ Tue, 30 Jun 2020 02:00:17: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 02:00:17: #2 alternative fragment length(s) may be 1,36 bps INFO @ Tue, 30 Jun 2020 02:00:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.20_model.r WARNING @ Tue, 30 Jun 2020 02:00:17: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:00:17: #2 You may need to consider one of the other alternative d(s): 1,36 WARNING @ Tue, 30 Jun 2020 02:00:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:00:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:00:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:00:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:00:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.05_summits.bed INFO @ Tue, 30 Jun 2020 02:00:19: Done! pass1 - making usageList (679 chroms): 1 millis pass2 - checking and writing primary data (4147 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:00:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:00:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:00:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:00:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.10_summits.bed INFO @ Tue, 30 Jun 2020 02:00:53: Done! pass1 - making usageList (459 chroms): 1 millis pass2 - checking and writing primary data (1435 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:01:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:01:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:01:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:01:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX159171/SRX159171.20_summits.bed INFO @ Tue, 30 Jun 2020 02:01:23: Done! pass1 - making usageList (147 chroms): 1 millis pass2 - checking and writing primary data (465 records, 4 fields): 7 millis CompletedMACS2peakCalling