Job ID = 6529725 SRX = SRX450797 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: 00:10:33 24024711 reads; of these: 24024711 (100.00%) were unpaired; of these: 1197426 (4.98%) aligned 0 times 20382101 (84.84%) aligned exactly 1 time 2445184 (10.18%) aligned >1 times 95.02% overall alignment rate Time searching: 00:10:33 Overall time: 00:10:33 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] 5335895 / 22827285 = 0.2338 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 03:39:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.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 03:39:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:39:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:39:39: 1000000 INFO @ Tue, 30 Jun 2020 03:39:50: 2000000 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 03:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.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 03:39:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:39:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:40:01: 3000000 INFO @ Tue, 30 Jun 2020 03:40:09: 1000000 INFO @ Tue, 30 Jun 2020 03:40:12: 4000000 INFO @ Tue, 30 Jun 2020 03:40:22: 2000000 INFO @ Tue, 30 Jun 2020 03:40:23: 5000000 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 03:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.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 03:40:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:40:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:40:34: 6000000 INFO @ Tue, 30 Jun 2020 03:40:34: 3000000 INFO @ Tue, 30 Jun 2020 03:40:38: 1000000 INFO @ Tue, 30 Jun 2020 03:40:45: 7000000 INFO @ Tue, 30 Jun 2020 03:40:45: 4000000 INFO @ Tue, 30 Jun 2020 03:40:50: 2000000 INFO @ Tue, 30 Jun 2020 03:40:55: 8000000 INFO @ Tue, 30 Jun 2020 03:40:56: 5000000 INFO @ Tue, 30 Jun 2020 03:41:02: 3000000 INFO @ Tue, 30 Jun 2020 03:41:06: 9000000 INFO @ Tue, 30 Jun 2020 03:41:07: 6000000 INFO @ Tue, 30 Jun 2020 03:41:13: 4000000 INFO @ Tue, 30 Jun 2020 03:41:16: 10000000 INFO @ Tue, 30 Jun 2020 03:41:17: 7000000 INFO @ Tue, 30 Jun 2020 03:41:24: 5000000 INFO @ Tue, 30 Jun 2020 03:41:26: 11000000 INFO @ Tue, 30 Jun 2020 03:41:27: 8000000 INFO @ Tue, 30 Jun 2020 03:41:36: 6000000 INFO @ Tue, 30 Jun 2020 03:41:36: 12000000 INFO @ Tue, 30 Jun 2020 03:41:37: 9000000 INFO @ Tue, 30 Jun 2020 03:41:45: 13000000 INFO @ Tue, 30 Jun 2020 03:41:46: 10000000 INFO @ Tue, 30 Jun 2020 03:41:47: 7000000 INFO @ Tue, 30 Jun 2020 03:41:54: 14000000 INFO @ Tue, 30 Jun 2020 03:41:55: 11000000 INFO @ Tue, 30 Jun 2020 03:41:58: 8000000 INFO @ Tue, 30 Jun 2020 03:42:03: 15000000 INFO @ Tue, 30 Jun 2020 03:42:03: 12000000 INFO @ Tue, 30 Jun 2020 03:42:10: 9000000 INFO @ Tue, 30 Jun 2020 03:42:12: 13000000 INFO @ Tue, 30 Jun 2020 03:42:12: 16000000 INFO @ Tue, 30 Jun 2020 03:42:21: 10000000 INFO @ Tue, 30 Jun 2020 03:42:22: 14000000 INFO @ Tue, 30 Jun 2020 03:42:22: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:42:27: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 03:42:27: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 03:42:27: #1 total tags in treatment: 17491390 INFO @ Tue, 30 Jun 2020 03:42:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:42:27: #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 03:42:28: #1 tags after filtering in treatment: 17491319 INFO @ Tue, 30 Jun 2020 03:42:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:42:28: #1 finished! INFO @ Tue, 30 Jun 2020 03:42:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:42:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:42:29: #2 number of paired peaks: 117 WARNING @ Tue, 30 Jun 2020 03:42:29: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 30 Jun 2020 03:42:29: start model_add_line... INFO @ Tue, 30 Jun 2020 03:42:29: start X-correlation... INFO @ Tue, 30 Jun 2020 03:42:29: end of X-cor INFO @ Tue, 30 Jun 2020 03:42:29: #2 finished! INFO @ Tue, 30 Jun 2020 03:42:29: #2 predicted fragment length is 103 bps INFO @ Tue, 30 Jun 2020 03:42:29: #2 alternative fragment length(s) may be 3,95,103,517,539 bps INFO @ Tue, 30 Jun 2020 03:42:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.05_model.r WARNING @ Tue, 30 Jun 2020 03:42:29: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:42:29: #2 You may need to consider one of the other alternative d(s): 3,95,103,517,539 WARNING @ Tue, 30 Jun 2020 03:42:29: #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 03:42:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:42:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:42:31: 15000000 INFO @ Tue, 30 Jun 2020 03:42:32: 11000000 INFO @ Tue, 30 Jun 2020 03:42:39: 16000000 INFO @ Tue, 30 Jun 2020 03:42:42: 12000000 INFO @ Tue, 30 Jun 2020 03:42:47: 17000000 INFO @ Tue, 30 Jun 2020 03:42:52: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 03:42:52: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 03:42:52: #1 total tags in treatment: 17491390 INFO @ Tue, 30 Jun 2020 03:42:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:42:52: #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 03:42:52: 13000000 INFO @ Tue, 30 Jun 2020 03:42:53: #1 tags after filtering in treatment: 17491319 INFO @ Tue, 30 Jun 2020 03:42:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:42:53: #1 finished! INFO @ Tue, 30 Jun 2020 03:42:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:42:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:42:54: #2 number of paired peaks: 117 WARNING @ Tue, 30 Jun 2020 03:42:54: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 30 Jun 2020 03:42:54: start model_add_line... INFO @ Tue, 30 Jun 2020 03:42:54: start X-correlation... INFO @ Tue, 30 Jun 2020 03:42:54: end of X-cor INFO @ Tue, 30 Jun 2020 03:42:54: #2 finished! INFO @ Tue, 30 Jun 2020 03:42:54: #2 predicted fragment length is 103 bps INFO @ Tue, 30 Jun 2020 03:42:54: #2 alternative fragment length(s) may be 3,95,103,517,539 bps INFO @ Tue, 30 Jun 2020 03:42:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.10_model.r WARNING @ Tue, 30 Jun 2020 03:42:54: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:42:54: #2 You may need to consider one of the other alternative d(s): 3,95,103,517,539 WARNING @ Tue, 30 Jun 2020 03:42:54: #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 03:42:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:42:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:43:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:43:03: 14000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:43:14: 15000000 INFO @ Tue, 30 Jun 2020 03:43:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:43:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:43:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.05_summits.bed INFO @ Tue, 30 Jun 2020 03:43:17: Done! pass1 - making usageList (106 chroms): 1 millis pass2 - checking and writing primary data (1367 records, 4 fields): 75 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:43:24: 16000000 INFO @ Tue, 30 Jun 2020 03:43:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:43:35: 17000000 INFO @ Tue, 30 Jun 2020 03:43:40: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 03:43:40: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 03:43:40: #1 total tags in treatment: 17491390 INFO @ Tue, 30 Jun 2020 03:43:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:43:40: #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 03:43:41: #1 tags after filtering in treatment: 17491319 INFO @ Tue, 30 Jun 2020 03:43:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:43:41: #1 finished! INFO @ Tue, 30 Jun 2020 03:43:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:43:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.10_summits.bed INFO @ Tue, 30 Jun 2020 03:43:41: Done! pass1 - making usageList (90 chroms): 1 millis pass2 - checking and writing primary data (291 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:43:42: #2 number of paired peaks: 117 WARNING @ Tue, 30 Jun 2020 03:43:42: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 30 Jun 2020 03:43:42: start model_add_line... INFO @ Tue, 30 Jun 2020 03:43:42: start X-correlation... INFO @ Tue, 30 Jun 2020 03:43:42: end of X-cor INFO @ Tue, 30 Jun 2020 03:43:42: #2 finished! INFO @ Tue, 30 Jun 2020 03:43:42: #2 predicted fragment length is 103 bps INFO @ Tue, 30 Jun 2020 03:43:42: #2 alternative fragment length(s) may be 3,95,103,517,539 bps INFO @ Tue, 30 Jun 2020 03:43:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.20_model.r WARNING @ Tue, 30 Jun 2020 03:43:42: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:43:42: #2 You may need to consider one of the other alternative d(s): 3,95,103,517,539 WARNING @ Tue, 30 Jun 2020 03:43:42: #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 03:43:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:43:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:44:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:44:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:44:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:44:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX450797/SRX450797.20_summits.bed INFO @ Tue, 30 Jun 2020 03:44:31: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 5 millis CompletedMACS2peakCalling