Job ID = 6529602 SRX = SRX336282 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: 00:03:37 14058991 reads; of these: 14058991 (100.00%) were unpaired; of these: 471710 (3.36%) aligned 0 times 9840029 (69.99%) aligned exactly 1 time 3747252 (26.65%) aligned >1 times 96.64% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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_rmdupse_core] 2874504 / 13587281 = 0.2116 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 02:22:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.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 02:22:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:22:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:22:32: 1000000 INFO @ Tue, 30 Jun 2020 02:22:39: 2000000 INFO @ Tue, 30 Jun 2020 02:22:46: 3000000 INFO @ Tue, 30 Jun 2020 02:22:53: 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 02:22:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.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 02:22:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:22:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:22:59: 5000000 INFO @ Tue, 30 Jun 2020 02:23:03: 1000000 INFO @ Tue, 30 Jun 2020 02:23:06: 6000000 INFO @ Tue, 30 Jun 2020 02:23:11: 2000000 INFO @ Tue, 30 Jun 2020 02:23:13: 7000000 INFO @ Tue, 30 Jun 2020 02:23:19: 3000000 INFO @ Tue, 30 Jun 2020 02:23:20: 8000000 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 02:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.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 02:23:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:23:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:23:26: 4000000 INFO @ Tue, 30 Jun 2020 02:23:27: 9000000 INFO @ Tue, 30 Jun 2020 02:23:33: 1000000 INFO @ Tue, 30 Jun 2020 02:23:33: 5000000 INFO @ Tue, 30 Jun 2020 02:23:34: 10000000 INFO @ Tue, 30 Jun 2020 02:23:39: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 02:23:39: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 02:23:39: #1 total tags in treatment: 10712777 INFO @ Tue, 30 Jun 2020 02:23:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:39: #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 02:23:40: 2000000 INFO @ Tue, 30 Jun 2020 02:23:40: #1 tags after filtering in treatment: 10712777 INFO @ Tue, 30 Jun 2020 02:23:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:40: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:40: 6000000 INFO @ Tue, 30 Jun 2020 02:23:41: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 02:23:41: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 02:23:41: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:41: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:41: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:41: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:41: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 02:23:41: #2 alternative fragment length(s) may be 4,11,35 bps INFO @ Tue, 30 Jun 2020 02:23:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.05_model.r WARNING @ Tue, 30 Jun 2020 02:23:41: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:23:41: #2 You may need to consider one of the other alternative d(s): 4,11,35 WARNING @ Tue, 30 Jun 2020 02:23:41: #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 02:23:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:23:46: 3000000 INFO @ Tue, 30 Jun 2020 02:23:47: 7000000 INFO @ Tue, 30 Jun 2020 02:23:52: 4000000 INFO @ Tue, 30 Jun 2020 02:23:53: 8000000 INFO @ Tue, 30 Jun 2020 02:23:59: 5000000 INFO @ Tue, 30 Jun 2020 02:24:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:01: 9000000 INFO @ Tue, 30 Jun 2020 02:24:05: 6000000 INFO @ Tue, 30 Jun 2020 02:24:08: 10000000 INFO @ Tue, 30 Jun 2020 02:24:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.05_summits.bed INFO @ Tue, 30 Jun 2020 02:24:11: 7000000 INFO @ Tue, 30 Jun 2020 02:24:11: Done! pass1 - making usageList (138 chroms): 1 millis pass2 - checking and writing primary data (386 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:24:14: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 02:24:14: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 02:24:14: #1 total tags in treatment: 10712777 INFO @ Tue, 30 Jun 2020 02:24:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:14: #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 02:24:15: #1 tags after filtering in treatment: 10712777 INFO @ Tue, 30 Jun 2020 02:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:15: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:16: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 02:24:16: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:16: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:16: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:16: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:16: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:16: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 02:24:16: #2 alternative fragment length(s) may be 4,11,35 bps INFO @ Tue, 30 Jun 2020 02:24:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.10_model.r WARNING @ Tue, 30 Jun 2020 02:24:16: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:24:16: #2 You may need to consider one of the other alternative d(s): 4,11,35 WARNING @ Tue, 30 Jun 2020 02:24:16: #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 02:24:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:17: 8000000 INFO @ Tue, 30 Jun 2020 02:24:24: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:24:30: 10000000 INFO @ Tue, 30 Jun 2020 02:24:35: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 02:24:35: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 02:24:35: #1 total tags in treatment: 10712777 INFO @ Tue, 30 Jun 2020 02:24:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:35: #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 02:24:35: #1 tags after filtering in treatment: 10712777 INFO @ Tue, 30 Jun 2020 02:24:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:35: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:36: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 02:24:36: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:36: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:36: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:36: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:36: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:36: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 02:24:36: #2 alternative fragment length(s) may be 4,11,35 bps INFO @ Tue, 30 Jun 2020 02:24:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.20_model.r WARNING @ Tue, 30 Jun 2020 02:24:36: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:24:36: #2 You may need to consider one of the other alternative d(s): 4,11,35 WARNING @ Tue, 30 Jun 2020 02:24:36: #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 02:24:36: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.10_summits.bed INFO @ Tue, 30 Jun 2020 02:24:46: Done! pass1 - making usageList (89 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:24:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:25:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX336282/SRX336282.20_summits.bed INFO @ Tue, 30 Jun 2020 02:25:06: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 3 millis CompletedMACS2peakCalling