Job ID = 6529870 SRX = SRX5343129 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: 00:12:59 31676150 reads; of these: 31676150 (100.00%) were unpaired; of these: 1378848 (4.35%) aligned 0 times 21015482 (66.34%) aligned exactly 1 time 9281820 (29.30%) aligned >1 times 95.65% overall alignment rate Time searching: 00:12:59 Overall time: 00:12:59 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 16 files... [bam_rmdupse_core] 4795830 / 30297302 = 0.1583 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 03:25:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.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 03:25:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:25:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:25:32: 1000000 INFO @ Tue, 30 Jun 2020 03:25:39: 2000000 INFO @ Tue, 30 Jun 2020 03:25:46: 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 03:25:52: 4000000 INFO @ Tue, 30 Jun 2020 03:25:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.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 03:25:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:25:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:25:59: 5000000 INFO @ Tue, 30 Jun 2020 03:26:03: 1000000 INFO @ Tue, 30 Jun 2020 03:26:06: 6000000 INFO @ Tue, 30 Jun 2020 03:26:12: 2000000 INFO @ Tue, 30 Jun 2020 03:26:13: 7000000 INFO @ Tue, 30 Jun 2020 03:26:19: 8000000 INFO @ Tue, 30 Jun 2020 03:26:20: 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 03:26:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.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 03:26:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:26:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:26:26: 9000000 INFO @ Tue, 30 Jun 2020 03:26:29: 4000000 INFO @ Tue, 30 Jun 2020 03:26:33: 10000000 INFO @ Tue, 30 Jun 2020 03:26:34: 1000000 INFO @ Tue, 30 Jun 2020 03:26:38: 5000000 INFO @ Tue, 30 Jun 2020 03:26:40: 11000000 INFO @ Tue, 30 Jun 2020 03:26:42: 2000000 INFO @ Tue, 30 Jun 2020 03:26:46: 6000000 INFO @ Tue, 30 Jun 2020 03:26:48: 12000000 INFO @ Tue, 30 Jun 2020 03:26:50: 3000000 INFO @ Tue, 30 Jun 2020 03:26:55: 7000000 INFO @ Tue, 30 Jun 2020 03:26:55: 13000000 INFO @ Tue, 30 Jun 2020 03:26:57: 4000000 INFO @ Tue, 30 Jun 2020 03:27:02: 14000000 INFO @ Tue, 30 Jun 2020 03:27:03: 8000000 INFO @ Tue, 30 Jun 2020 03:27:05: 5000000 INFO @ Tue, 30 Jun 2020 03:27:10: 15000000 INFO @ Tue, 30 Jun 2020 03:27:12: 9000000 INFO @ Tue, 30 Jun 2020 03:27:13: 6000000 INFO @ Tue, 30 Jun 2020 03:27:17: 16000000 INFO @ Tue, 30 Jun 2020 03:27:20: 10000000 INFO @ Tue, 30 Jun 2020 03:27:20: 7000000 INFO @ Tue, 30 Jun 2020 03:27:25: 17000000 INFO @ Tue, 30 Jun 2020 03:27:28: 8000000 INFO @ Tue, 30 Jun 2020 03:27:29: 11000000 INFO @ Tue, 30 Jun 2020 03:27:32: 18000000 INFO @ Tue, 30 Jun 2020 03:27:35: 9000000 INFO @ Tue, 30 Jun 2020 03:27:38: 12000000 INFO @ Tue, 30 Jun 2020 03:27:41: 19000000 INFO @ Tue, 30 Jun 2020 03:27:42: 10000000 INFO @ Tue, 30 Jun 2020 03:27:46: 13000000 INFO @ Tue, 30 Jun 2020 03:27:50: 11000000 INFO @ Tue, 30 Jun 2020 03:27:50: 20000000 INFO @ Tue, 30 Jun 2020 03:27:54: 14000000 INFO @ Tue, 30 Jun 2020 03:27:57: 12000000 INFO @ Tue, 30 Jun 2020 03:27:58: 21000000 INFO @ Tue, 30 Jun 2020 03:28:03: 15000000 INFO @ Tue, 30 Jun 2020 03:28:04: 13000000 INFO @ Tue, 30 Jun 2020 03:28:08: 22000000 INFO @ Tue, 30 Jun 2020 03:28:10: 14000000 INFO @ Tue, 30 Jun 2020 03:28:12: 16000000 INFO @ Tue, 30 Jun 2020 03:28:16: 23000000 INFO @ Tue, 30 Jun 2020 03:28:18: 15000000 INFO @ Tue, 30 Jun 2020 03:28:20: 17000000 INFO @ Tue, 30 Jun 2020 03:28:25: 16000000 INFO @ Tue, 30 Jun 2020 03:28:25: 24000000 INFO @ Tue, 30 Jun 2020 03:28:29: 18000000 INFO @ Tue, 30 Jun 2020 03:28:32: 17000000 INFO @ Tue, 30 Jun 2020 03:28:33: 25000000 INFO @ Tue, 30 Jun 2020 03:28:37: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:28:37: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:28:37: #1 total tags in treatment: 25501472 INFO @ Tue, 30 Jun 2020 03:28:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:28:37: #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 03:28:37: 19000000 INFO @ Tue, 30 Jun 2020 03:28:38: #1 tags after filtering in treatment: 25501469 INFO @ Tue, 30 Jun 2020 03:28:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:28:38: #1 finished! INFO @ Tue, 30 Jun 2020 03:28:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:28:39: 18000000 INFO @ Tue, 30 Jun 2020 03:28:40: #2 number of paired peaks: 208 WARNING @ Tue, 30 Jun 2020 03:28:40: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 30 Jun 2020 03:28:40: start model_add_line... INFO @ Tue, 30 Jun 2020 03:28:40: start X-correlation... INFO @ Tue, 30 Jun 2020 03:28:40: end of X-cor INFO @ Tue, 30 Jun 2020 03:28:40: #2 finished! INFO @ Tue, 30 Jun 2020 03:28:40: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 03:28:40: #2 alternative fragment length(s) may be 2,30,53 bps INFO @ Tue, 30 Jun 2020 03:28:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.05_model.r WARNING @ Tue, 30 Jun 2020 03:28:40: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:28:40: #2 You may need to consider one of the other alternative d(s): 2,30,53 WARNING @ Tue, 30 Jun 2020 03:28:40: #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 03:28:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:28:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:28:46: 20000000 INFO @ Tue, 30 Jun 2020 03:28:46: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:28:52: 20000000 INFO @ Tue, 30 Jun 2020 03:28:54: 21000000 INFO @ Tue, 30 Jun 2020 03:28:59: 21000000 INFO @ Tue, 30 Jun 2020 03:29:03: 22000000 INFO @ Tue, 30 Jun 2020 03:29:08: 22000000 INFO @ Tue, 30 Jun 2020 03:29:12: 23000000 INFO @ Tue, 30 Jun 2020 03:29:15: 23000000 INFO @ Tue, 30 Jun 2020 03:29:20: 24000000 INFO @ Tue, 30 Jun 2020 03:29:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:29:22: 24000000 INFO @ Tue, 30 Jun 2020 03:29:29: 25000000 INFO @ Tue, 30 Jun 2020 03:29:30: 25000000 INFO @ Tue, 30 Jun 2020 03:29:33: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:29:33: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:29:33: #1 total tags in treatment: 25501472 INFO @ Tue, 30 Jun 2020 03:29:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:29:33: #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 03:29:34: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:29:34: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:29:34: #1 total tags in treatment: 25501472 INFO @ Tue, 30 Jun 2020 03:29:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:29:34: #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 03:29:34: #1 tags after filtering in treatment: 25501469 INFO @ Tue, 30 Jun 2020 03:29:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:29:34: #1 finished! INFO @ Tue, 30 Jun 2020 03:29:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:29:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:29:35: #1 tags after filtering in treatment: 25501469 INFO @ Tue, 30 Jun 2020 03:29:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:29:35: #1 finished! INFO @ Tue, 30 Jun 2020 03:29:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:29:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:29:36: #2 number of paired peaks: 208 WARNING @ Tue, 30 Jun 2020 03:29:36: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 30 Jun 2020 03:29:36: start model_add_line... INFO @ Tue, 30 Jun 2020 03:29:36: start X-correlation... INFO @ Tue, 30 Jun 2020 03:29:36: end of X-cor INFO @ Tue, 30 Jun 2020 03:29:36: #2 finished! INFO @ Tue, 30 Jun 2020 03:29:36: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 03:29:36: #2 alternative fragment length(s) may be 2,30,53 bps INFO @ Tue, 30 Jun 2020 03:29:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.10_model.r WARNING @ Tue, 30 Jun 2020 03:29:36: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:29:36: #2 You may need to consider one of the other alternative d(s): 2,30,53 WARNING @ Tue, 30 Jun 2020 03:29:36: #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 03:29:36: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:29:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:29:37: #2 number of paired peaks: 208 WARNING @ Tue, 30 Jun 2020 03:29:37: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 30 Jun 2020 03:29:37: start model_add_line... INFO @ Tue, 30 Jun 2020 03:29:37: start X-correlation... INFO @ Tue, 30 Jun 2020 03:29:37: end of X-cor INFO @ Tue, 30 Jun 2020 03:29:37: #2 finished! INFO @ Tue, 30 Jun 2020 03:29:37: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 03:29:37: #2 alternative fragment length(s) may be 2,30,53 bps INFO @ Tue, 30 Jun 2020 03:29:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.20_model.r WARNING @ Tue, 30 Jun 2020 03:29:37: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:29:37: #2 You may need to consider one of the other alternative d(s): 2,30,53 WARNING @ Tue, 30 Jun 2020 03:29:37: #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 03:29:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:29:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:29:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:29:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:29:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.05_summits.bed INFO @ Tue, 30 Jun 2020 03:29:41: Done! pass1 - making usageList (782 chroms): 2 millis pass2 - checking and writing primary data (2711 records, 4 fields): 44 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:30:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:30:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:30:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:30:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:30:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.10_summits.bed INFO @ Tue, 30 Jun 2020 03:30:37: Done! pass1 - making usageList (603 chroms): 1 millis pass2 - checking and writing primary data (1897 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:30:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:30:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:30:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343129/SRX5343129.20_summits.bed INFO @ Tue, 30 Jun 2020 03:30:38: Done! pass1 - making usageList (389 chroms): 1 millis pass2 - checking and writing primary data (854 records, 4 fields): 22 millis CompletedMACS2peakCalling