Job ID = 6530111 SRX = SRX992690 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: 00:06:39 32113401 reads; of these: 32113401 (100.00%) were unpaired; of these: 11624779 (36.20%) aligned 0 times 15299835 (47.64%) aligned exactly 1 time 5188787 (16.16%) aligned >1 times 63.80% overall alignment rate Time searching: 00:06:39 Overall time: 00:06:39 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] 2711186 / 20488622 = 0.1323 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 03:28:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.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 03:28:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:28:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:29:00: 1000000 INFO @ Tue, 30 Jun 2020 03:29:06: 2000000 INFO @ Tue, 30 Jun 2020 03:29:12: 3000000 INFO @ Tue, 30 Jun 2020 03:29:17: 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 03:29:23: 5000000 INFO @ Tue, 30 Jun 2020 03:29:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.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 03:29:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:29:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:29:30: 6000000 INFO @ Tue, 30 Jun 2020 03:29:30: 1000000 INFO @ Tue, 30 Jun 2020 03:29:37: 7000000 INFO @ Tue, 30 Jun 2020 03:29:37: 2000000 INFO @ Tue, 30 Jun 2020 03:29:43: 8000000 INFO @ Tue, 30 Jun 2020 03:29:44: 3000000 INFO @ Tue, 30 Jun 2020 03:29:50: 9000000 INFO @ Tue, 30 Jun 2020 03:29:51: 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 03:29:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.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 03:29:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:29:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:29:57: 10000000 INFO @ Tue, 30 Jun 2020 03:29:57: 5000000 INFO @ Tue, 30 Jun 2020 03:30:01: 1000000 INFO @ Tue, 30 Jun 2020 03:30:03: 11000000 INFO @ Tue, 30 Jun 2020 03:30:04: 6000000 INFO @ Tue, 30 Jun 2020 03:30:08: 2000000 INFO @ Tue, 30 Jun 2020 03:30:10: 12000000 INFO @ Tue, 30 Jun 2020 03:30:11: 7000000 INFO @ Tue, 30 Jun 2020 03:30:15: 3000000 INFO @ Tue, 30 Jun 2020 03:30:17: 13000000 INFO @ Tue, 30 Jun 2020 03:30:18: 8000000 INFO @ Tue, 30 Jun 2020 03:30:21: 4000000 INFO @ Tue, 30 Jun 2020 03:30:24: 14000000 INFO @ Tue, 30 Jun 2020 03:30:25: 9000000 INFO @ Tue, 30 Jun 2020 03:30:28: 5000000 INFO @ Tue, 30 Jun 2020 03:30:31: 15000000 INFO @ Tue, 30 Jun 2020 03:30:32: 10000000 INFO @ Tue, 30 Jun 2020 03:30:35: 6000000 INFO @ Tue, 30 Jun 2020 03:30:38: 16000000 INFO @ Tue, 30 Jun 2020 03:30:39: 11000000 INFO @ Tue, 30 Jun 2020 03:30:42: 7000000 INFO @ Tue, 30 Jun 2020 03:30:45: 17000000 INFO @ Tue, 30 Jun 2020 03:30:46: 12000000 INFO @ Tue, 30 Jun 2020 03:30:49: 8000000 INFO @ Tue, 30 Jun 2020 03:30:50: #1 tag size is determined as 54 bps INFO @ Tue, 30 Jun 2020 03:30:50: #1 tag size = 54 INFO @ Tue, 30 Jun 2020 03:30:50: #1 total tags in treatment: 17777436 INFO @ Tue, 30 Jun 2020 03:30:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:30:50: #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 03:30:51: #1 tags after filtering in treatment: 17777435 INFO @ Tue, 30 Jun 2020 03:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:30:51: #1 finished! INFO @ Tue, 30 Jun 2020 03:30:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:30:52: #2 number of paired peaks: 389 WARNING @ Tue, 30 Jun 2020 03:30:52: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Tue, 30 Jun 2020 03:30:52: start model_add_line... INFO @ Tue, 30 Jun 2020 03:30:52: start X-correlation... INFO @ Tue, 30 Jun 2020 03:30:52: end of X-cor INFO @ Tue, 30 Jun 2020 03:30:52: #2 finished! INFO @ Tue, 30 Jun 2020 03:30:52: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:30:52: #2 alternative fragment length(s) may be 4,52 bps INFO @ Tue, 30 Jun 2020 03:30:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.05_model.r WARNING @ Tue, 30 Jun 2020 03:30:52: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:30:52: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Tue, 30 Jun 2020 03:30:52: #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 03:30:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:30:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:30:53: 13000000 INFO @ Tue, 30 Jun 2020 03:30:56: 9000000 INFO @ Tue, 30 Jun 2020 03:30:59: 14000000 INFO @ Tue, 30 Jun 2020 03:31:03: 10000000 INFO @ Tue, 30 Jun 2020 03:31:07: 15000000 INFO @ Tue, 30 Jun 2020 03:31:10: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:31:14: 16000000 INFO @ Tue, 30 Jun 2020 03:31:17: 12000000 INFO @ Tue, 30 Jun 2020 03:31:21: 17000000 INFO @ Tue, 30 Jun 2020 03:31:24: 13000000 INFO @ Tue, 30 Jun 2020 03:31:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:31:26: #1 tag size is determined as 54 bps INFO @ Tue, 30 Jun 2020 03:31:26: #1 tag size = 54 INFO @ Tue, 30 Jun 2020 03:31:26: #1 total tags in treatment: 17777436 INFO @ Tue, 30 Jun 2020 03:31:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:31:26: #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 03:31:27: #1 tags after filtering in treatment: 17777435 INFO @ Tue, 30 Jun 2020 03:31:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:31:27: #1 finished! INFO @ Tue, 30 Jun 2020 03:31:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:31:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:31:28: #2 number of paired peaks: 389 WARNING @ Tue, 30 Jun 2020 03:31:28: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Tue, 30 Jun 2020 03:31:28: start model_add_line... INFO @ Tue, 30 Jun 2020 03:31:28: start X-correlation... INFO @ Tue, 30 Jun 2020 03:31:28: end of X-cor INFO @ Tue, 30 Jun 2020 03:31:28: #2 finished! INFO @ Tue, 30 Jun 2020 03:31:28: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:31:28: #2 alternative fragment length(s) may be 4,52 bps INFO @ Tue, 30 Jun 2020 03:31:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.10_model.r WARNING @ Tue, 30 Jun 2020 03:31:28: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:31:28: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Tue, 30 Jun 2020 03:31:28: #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 03:31:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:31:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:31:31: 14000000 INFO @ Tue, 30 Jun 2020 03:31:37: 15000000 INFO @ Tue, 30 Jun 2020 03:31:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:31:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:31:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.05_summits.bed INFO @ Tue, 30 Jun 2020 03:31:41: Done! pass1 - making usageList (668 chroms): 1 millis pass2 - checking and writing primary data (2705 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:31:44: 16000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:31:50: 17000000 INFO @ Tue, 30 Jun 2020 03:31:55: #1 tag size is determined as 54 bps INFO @ Tue, 30 Jun 2020 03:31:55: #1 tag size = 54 INFO @ Tue, 30 Jun 2020 03:31:55: #1 total tags in treatment: 17777436 INFO @ Tue, 30 Jun 2020 03:31:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:31:55: #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 03:31:55: #1 tags after filtering in treatment: 17777435 INFO @ Tue, 30 Jun 2020 03:31:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:31:55: #1 finished! INFO @ Tue, 30 Jun 2020 03:31:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:31:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:31:57: #2 number of paired peaks: 389 WARNING @ Tue, 30 Jun 2020 03:31:57: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Tue, 30 Jun 2020 03:31:57: start model_add_line... INFO @ Tue, 30 Jun 2020 03:31:57: start X-correlation... INFO @ Tue, 30 Jun 2020 03:31:57: end of X-cor INFO @ Tue, 30 Jun 2020 03:31:57: #2 finished! INFO @ Tue, 30 Jun 2020 03:31:57: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:31:57: #2 alternative fragment length(s) may be 4,52 bps INFO @ Tue, 30 Jun 2020 03:31:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.20_model.r WARNING @ Tue, 30 Jun 2020 03:31:57: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:31:57: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Tue, 30 Jun 2020 03:31:57: #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 03:31:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:31:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:32:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:32:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:32:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:32:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.10_summits.bed INFO @ Tue, 30 Jun 2020 03:32:17: Done! pass1 - making usageList (452 chroms): 1 millis pass2 - checking and writing primary data (1355 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:32:30: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:32:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:32:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:32:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX992690/SRX992690.20_summits.bed INFO @ Tue, 30 Jun 2020 03:32:45: Done! pass1 - making usageList (222 chroms): 1 millis pass2 - checking and writing primary data (484 records, 4 fields): 6 millis CompletedMACS2peakCalling