Job ID = 16439572 SRX = SRX15206476 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: 00:30:15 39048114 reads; of these: 39048114 (100.00%) were unpaired; of these: 1947213 (4.99%) aligned 0 times 31917772 (81.74%) aligned exactly 1 time 5183129 (13.27%) aligned >1 times 95.01% overall alignment rate Time searching: 00:30:16 Overall time: 00:30:16 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 28 files... [bam_rmdupse_core] 12421254 / 37100901 = 0.3348 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:23:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.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, 02 Aug 2022 16:23:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:23:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:23:54: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:24:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.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, 02 Aug 2022 16:24:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:24:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:24:12: 2000000 INFO @ Tue, 02 Aug 2022 16:24:23: 1000000 INFO @ Tue, 02 Aug 2022 16:24:30: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.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, 02 Aug 2022 16:24:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:24:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:24:39: 2000000 INFO @ Tue, 02 Aug 2022 16:24:49: 4000000 INFO @ Tue, 02 Aug 2022 16:24:54: 1000000 INFO @ Tue, 02 Aug 2022 16:24:55: 3000000 INFO @ Tue, 02 Aug 2022 16:25:08: 5000000 INFO @ Tue, 02 Aug 2022 16:25:12: 4000000 INFO @ Tue, 02 Aug 2022 16:25:13: 2000000 INFO @ Tue, 02 Aug 2022 16:25:27: 6000000 INFO @ Tue, 02 Aug 2022 16:25:28: 5000000 INFO @ Tue, 02 Aug 2022 16:25:31: 3000000 INFO @ Tue, 02 Aug 2022 16:25:45: 6000000 INFO @ Tue, 02 Aug 2022 16:25:46: 7000000 INFO @ Tue, 02 Aug 2022 16:25:50: 4000000 INFO @ Tue, 02 Aug 2022 16:26:02: 7000000 INFO @ Tue, 02 Aug 2022 16:26:05: 8000000 INFO @ Tue, 02 Aug 2022 16:26:08: 5000000 INFO @ Tue, 02 Aug 2022 16:26:19: 8000000 INFO @ Tue, 02 Aug 2022 16:26:25: 9000000 INFO @ Tue, 02 Aug 2022 16:26:26: 6000000 INFO @ Tue, 02 Aug 2022 16:26:36: 9000000 INFO @ Tue, 02 Aug 2022 16:26:44: 7000000 INFO @ Tue, 02 Aug 2022 16:26:44: 10000000 INFO @ Tue, 02 Aug 2022 16:26:53: 10000000 INFO @ Tue, 02 Aug 2022 16:27:02: 8000000 INFO @ Tue, 02 Aug 2022 16:27:04: 11000000 INFO @ Tue, 02 Aug 2022 16:27:10: 11000000 INFO @ Tue, 02 Aug 2022 16:27:20: 9000000 INFO @ Tue, 02 Aug 2022 16:27:23: 12000000 INFO @ Tue, 02 Aug 2022 16:27:27: 12000000 INFO @ Tue, 02 Aug 2022 16:27:37: 10000000 INFO @ Tue, 02 Aug 2022 16:27:41: 13000000 INFO @ Tue, 02 Aug 2022 16:27:44: 13000000 INFO @ Tue, 02 Aug 2022 16:27:54: 11000000 INFO @ Tue, 02 Aug 2022 16:28:01: 14000000 INFO @ Tue, 02 Aug 2022 16:28:01: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:28:11: 12000000 INFO @ Tue, 02 Aug 2022 16:28:17: 15000000 INFO @ Tue, 02 Aug 2022 16:28:20: 15000000 INFO @ Tue, 02 Aug 2022 16:28:29: 13000000 INFO @ Tue, 02 Aug 2022 16:28:34: 16000000 INFO @ Tue, 02 Aug 2022 16:28:38: 16000000 INFO @ Tue, 02 Aug 2022 16:28:47: 14000000 INFO @ Tue, 02 Aug 2022 16:28:50: 17000000 INFO @ Tue, 02 Aug 2022 16:28:57: 17000000 INFO @ Tue, 02 Aug 2022 16:29:04: 15000000 INFO @ Tue, 02 Aug 2022 16:29:07: 18000000 INFO @ Tue, 02 Aug 2022 16:29:16: 18000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:29:21: 16000000 INFO @ Tue, 02 Aug 2022 16:29:24: 19000000 INFO @ Tue, 02 Aug 2022 16:29:34: 19000000 INFO @ Tue, 02 Aug 2022 16:29:38: 17000000 INFO @ Tue, 02 Aug 2022 16:29:42: 20000000 INFO @ Tue, 02 Aug 2022 16:29:54: 20000000 INFO @ Tue, 02 Aug 2022 16:29:56: 18000000 INFO @ Tue, 02 Aug 2022 16:29:59: 21000000 INFO @ Tue, 02 Aug 2022 16:30:14: 19000000 INFO @ Tue, 02 Aug 2022 16:30:14: 21000000 INFO @ Tue, 02 Aug 2022 16:30:17: 22000000 INFO @ Tue, 02 Aug 2022 16:30:33: 20000000 INFO @ Tue, 02 Aug 2022 16:30:34: 22000000 INFO @ Tue, 02 Aug 2022 16:30:35: 23000000 INFO @ Tue, 02 Aug 2022 16:30:51: 21000000 INFO @ Tue, 02 Aug 2022 16:30:53: 24000000 INFO @ Tue, 02 Aug 2022 16:30:54: 23000000 INFO @ Tue, 02 Aug 2022 16:31:06: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:31:06: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:31:06: #1 total tags in treatment: 24679647 INFO @ Tue, 02 Aug 2022 16:31:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:31:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:31:07: #1 tags after filtering in treatment: 24679390 INFO @ Tue, 02 Aug 2022 16:31:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:31:07: #1 finished! INFO @ Tue, 02 Aug 2022 16:31:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:31:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:31:08: #2 number of paired peaks: 196 WARNING @ Tue, 02 Aug 2022 16:31:08: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 02 Aug 2022 16:31:08: start model_add_line... INFO @ Tue, 02 Aug 2022 16:31:08: 22000000 INFO @ Tue, 02 Aug 2022 16:31:09: start X-correlation... INFO @ Tue, 02 Aug 2022 16:31:09: end of X-cor INFO @ Tue, 02 Aug 2022 16:31:09: #2 finished! INFO @ Tue, 02 Aug 2022 16:31:09: #2 predicted fragment length is 132 bps INFO @ Tue, 02 Aug 2022 16:31:09: #2 alternative fragment length(s) may be 2,132 bps INFO @ Tue, 02 Aug 2022 16:31:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.10_model.r WARNING @ Tue, 02 Aug 2022 16:31:09: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:31:09: #2 You may need to consider one of the other alternative d(s): 2,132 WARNING @ Tue, 02 Aug 2022 16:31:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:31:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:31:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:31:14: 24000000 INFO @ Tue, 02 Aug 2022 16:31:26: 23000000 INFO @ Tue, 02 Aug 2022 16:31:27: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:31:27: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:31:27: #1 total tags in treatment: 24679647 INFO @ Tue, 02 Aug 2022 16:31:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:31:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:31:28: #1 tags after filtering in treatment: 24679390 INFO @ Tue, 02 Aug 2022 16:31:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:31:28: #1 finished! INFO @ Tue, 02 Aug 2022 16:31:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:31:30: #2 number of paired peaks: 196 WARNING @ Tue, 02 Aug 2022 16:31:30: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 02 Aug 2022 16:31:30: start model_add_line... INFO @ Tue, 02 Aug 2022 16:31:30: start X-correlation... INFO @ Tue, 02 Aug 2022 16:31:30: end of X-cor INFO @ Tue, 02 Aug 2022 16:31:30: #2 finished! INFO @ Tue, 02 Aug 2022 16:31:30: #2 predicted fragment length is 132 bps INFO @ Tue, 02 Aug 2022 16:31:30: #2 alternative fragment length(s) may be 2,132 bps INFO @ Tue, 02 Aug 2022 16:31:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.05_model.r WARNING @ Tue, 02 Aug 2022 16:31:30: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:31:30: #2 You may need to consider one of the other alternative d(s): 2,132 WARNING @ Tue, 02 Aug 2022 16:31:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:31:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:31:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:31:46: 24000000 INFO @ Tue, 02 Aug 2022 16:31:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:31:58: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:31:58: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:31:58: #1 total tags in treatment: 24679647 INFO @ Tue, 02 Aug 2022 16:31:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:31:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:31:59: #1 tags after filtering in treatment: 24679390 INFO @ Tue, 02 Aug 2022 16:31:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:31:59: #1 finished! INFO @ Tue, 02 Aug 2022 16:31:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:31:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:32:01: #2 number of paired peaks: 196 WARNING @ Tue, 02 Aug 2022 16:32:01: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 02 Aug 2022 16:32:01: start model_add_line... INFO @ Tue, 02 Aug 2022 16:32:01: start X-correlation... INFO @ Tue, 02 Aug 2022 16:32:01: end of X-cor INFO @ Tue, 02 Aug 2022 16:32:01: #2 finished! INFO @ Tue, 02 Aug 2022 16:32:01: #2 predicted fragment length is 132 bps INFO @ Tue, 02 Aug 2022 16:32:01: #2 alternative fragment length(s) may be 2,132 bps INFO @ Tue, 02 Aug 2022 16:32:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.20_model.r WARNING @ Tue, 02 Aug 2022 16:32:01: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:32:01: #2 You may need to consider one of the other alternative d(s): 2,132 WARNING @ Tue, 02 Aug 2022 16:32:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:32:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:32:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:32:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:32:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:32:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:32:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.10_summits.bed INFO @ Tue, 02 Aug 2022 16:32:16: Done! pass1 - making usageList (346 chroms): 2 millis pass2 - checking and writing primary data (669 records, 4 fields): 143 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:32:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:32:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:32:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.05_summits.bed INFO @ Tue, 02 Aug 2022 16:32:37: Done! pass1 - making usageList (406 chroms): 1 millis pass2 - checking and writing primary data (897 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:32:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:33:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:33:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:33:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206476/SRX15206476.20_summits.bed INFO @ Tue, 02 Aug 2022 16:33:08: Done! pass1 - making usageList (275 chroms): 2 millis pass2 - checking and writing primary data (452 records, 4 fields): 66 millis CompletedMACS2peakCalling