Job ID = 6530088 SRX = SRX7672889 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: 00:05:18 20092910 reads; of these: 20092910 (100.00%) were unpaired; of these: 2548211 (12.68%) aligned 0 times 12744526 (63.43%) aligned exactly 1 time 4800173 (23.89%) aligned >1 times 87.32% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 2006223 / 17544699 = 0.1143 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 03:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.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 03:29:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:29:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:29:32: 1000000 INFO @ Tue, 30 Jun 2020 03:29:40: 2000000 INFO @ Tue, 30 Jun 2020 03:29:47: 3000000 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 03:29:55: 4000000 INFO @ Tue, 30 Jun 2020 03:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.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 03:29:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:29:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:30:03: 5000000 INFO @ Tue, 30 Jun 2020 03:30:03: 1000000 INFO @ Tue, 30 Jun 2020 03:30:11: 6000000 INFO @ Tue, 30 Jun 2020 03:30:12: 2000000 INFO @ Tue, 30 Jun 2020 03:30:20: 7000000 INFO @ Tue, 30 Jun 2020 03:30:20: 3000000 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 03:30:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.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 03:30:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:30:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:30:28: 8000000 INFO @ Tue, 30 Jun 2020 03:30:29: 4000000 INFO @ Tue, 30 Jun 2020 03:30:34: 1000000 INFO @ Tue, 30 Jun 2020 03:30:37: 9000000 INFO @ Tue, 30 Jun 2020 03:30:37: 5000000 INFO @ Tue, 30 Jun 2020 03:30:42: 2000000 INFO @ Tue, 30 Jun 2020 03:30:45: 10000000 INFO @ Tue, 30 Jun 2020 03:30:45: 6000000 INFO @ Tue, 30 Jun 2020 03:30:51: 3000000 INFO @ Tue, 30 Jun 2020 03:30:54: 11000000 INFO @ Tue, 30 Jun 2020 03:30:54: 7000000 INFO @ Tue, 30 Jun 2020 03:31:00: 4000000 INFO @ Tue, 30 Jun 2020 03:31:02: 8000000 INFO @ Tue, 30 Jun 2020 03:31:02: 12000000 INFO @ Tue, 30 Jun 2020 03:31:08: 5000000 INFO @ Tue, 30 Jun 2020 03:31:11: 9000000 INFO @ Tue, 30 Jun 2020 03:31:11: 13000000 INFO @ Tue, 30 Jun 2020 03:31:17: 6000000 INFO @ Tue, 30 Jun 2020 03:31:19: 10000000 INFO @ Tue, 30 Jun 2020 03:31:20: 14000000 INFO @ Tue, 30 Jun 2020 03:31:25: 7000000 INFO @ Tue, 30 Jun 2020 03:31:27: 11000000 INFO @ Tue, 30 Jun 2020 03:31:28: 15000000 INFO @ Tue, 30 Jun 2020 03:31:33: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:31:33: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:31:33: #1 total tags in treatment: 15538476 INFO @ Tue, 30 Jun 2020 03:31:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:31:33: #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 03:31:34: #1 tags after filtering in treatment: 15538476 INFO @ Tue, 30 Jun 2020 03:31:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:31:34: #1 finished! INFO @ Tue, 30 Jun 2020 03:31:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:31:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:31:34: 8000000 INFO @ Tue, 30 Jun 2020 03:31:35: #2 number of paired peaks: 428 WARNING @ Tue, 30 Jun 2020 03:31:35: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 30 Jun 2020 03:31:35: start model_add_line... INFO @ Tue, 30 Jun 2020 03:31:35: start X-correlation... INFO @ Tue, 30 Jun 2020 03:31:35: end of X-cor INFO @ Tue, 30 Jun 2020 03:31:35: #2 finished! INFO @ Tue, 30 Jun 2020 03:31:35: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 03:31:35: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 30 Jun 2020 03:31:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.05_model.r WARNING @ Tue, 30 Jun 2020 03:31:35: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:31:35: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 30 Jun 2020 03:31:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:31:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:31:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:31:36: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:31:42: 9000000 INFO @ Tue, 30 Jun 2020 03:31:45: 13000000 INFO @ Tue, 30 Jun 2020 03:31:50: 10000000 INFO @ Tue, 30 Jun 2020 03:31:53: 14000000 INFO @ Tue, 30 Jun 2020 03:31:58: 11000000 INFO @ Tue, 30 Jun 2020 03:32:01: 15000000 INFO @ Tue, 30 Jun 2020 03:32:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:32:06: 12000000 INFO @ Tue, 30 Jun 2020 03:32:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:32:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:32:06: #1 total tags in treatment: 15538476 INFO @ Tue, 30 Jun 2020 03:32:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:32:06: #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 03:32:06: #1 tags after filtering in treatment: 15538476 INFO @ Tue, 30 Jun 2020 03:32:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:32:06: #1 finished! INFO @ Tue, 30 Jun 2020 03:32:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:32:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:32:07: #2 number of paired peaks: 428 WARNING @ Tue, 30 Jun 2020 03:32:07: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 30 Jun 2020 03:32:07: start model_add_line... INFO @ Tue, 30 Jun 2020 03:32:07: start X-correlation... INFO @ Tue, 30 Jun 2020 03:32:07: end of X-cor INFO @ Tue, 30 Jun 2020 03:32:07: #2 finished! INFO @ Tue, 30 Jun 2020 03:32:07: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 03:32:07: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 30 Jun 2020 03:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.10_model.r WARNING @ Tue, 30 Jun 2020 03:32:07: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:32:07: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 30 Jun 2020 03:32:07: #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 03:32:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:32:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:32:13: 13000000 INFO @ Tue, 30 Jun 2020 03:32:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:32:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:32:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.05_summits.bed INFO @ Tue, 30 Jun 2020 03:32:19: Done! pass1 - making usageList (640 chroms): 1 millis pass2 - checking and writing primary data (2476 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:32:21: 14000000 INFO @ Tue, 30 Jun 2020 03:32:28: 15000000 INFO @ Tue, 30 Jun 2020 03:32:32: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:32:32: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:32:32: #1 total tags in treatment: 15538476 INFO @ Tue, 30 Jun 2020 03:32:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:32:32: #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 03:32:32: #1 tags after filtering in treatment: 15538476 INFO @ Tue, 30 Jun 2020 03:32:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:32:32: #1 finished! INFO @ Tue, 30 Jun 2020 03:32:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:32:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:32:33: #2 number of paired peaks: 428 WARNING @ Tue, 30 Jun 2020 03:32:33: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 30 Jun 2020 03:32:33: start model_add_line... INFO @ Tue, 30 Jun 2020 03:32:33: start X-correlation... INFO @ Tue, 30 Jun 2020 03:32:33: end of X-cor INFO @ Tue, 30 Jun 2020 03:32:33: #2 finished! INFO @ Tue, 30 Jun 2020 03:32:33: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 03:32:33: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 30 Jun 2020 03:32:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.20_model.r WARNING @ Tue, 30 Jun 2020 03:32:33: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:32:33: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 30 Jun 2020 03:32:33: #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 03:32:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:32:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:32:37: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:32:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:32:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:32:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.10_summits.bed INFO @ Tue, 30 Jun 2020 03:32:51: Done! pass1 - making usageList (510 chroms): 1 millis pass2 - checking and writing primary data (1827 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:33:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:33:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:33:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:33:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7672889/SRX7672889.20_summits.bed INFO @ Tue, 30 Jun 2020 03:33:15: Done! pass1 - making usageList (269 chroms): 1 millis pass2 - checking and writing primary data (573 records, 4 fields): 8 millis CompletedMACS2peakCalling