Job ID = 6529596 SRX = SRX331409 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: 00:05:16 19200904 reads; of these: 19200904 (100.00%) were unpaired; of these: 1306520 (6.80%) aligned 0 times 13670326 (71.20%) aligned exactly 1 time 4224058 (22.00%) aligned >1 times 93.20% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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 8 files... [bam_rmdupse_core] 1808680 / 17894384 = 0.1011 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 02:39:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.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 02:39:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:39:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:39:35: 1000000 INFO @ Tue, 30 Jun 2020 02:39:42: 2000000 INFO @ Tue, 30 Jun 2020 02:39:49: 3000000 INFO @ Tue, 30 Jun 2020 02:39:55: 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 02:39:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.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 02:39:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:39:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:40:02: 5000000 INFO @ Tue, 30 Jun 2020 02:40:05: 1000000 INFO @ Tue, 30 Jun 2020 02:40:08: 6000000 INFO @ Tue, 30 Jun 2020 02:40:12: 2000000 INFO @ Tue, 30 Jun 2020 02:40:14: 7000000 INFO @ Tue, 30 Jun 2020 02:40:18: 3000000 INFO @ Tue, 30 Jun 2020 02:40:21: 8000000 INFO @ Tue, 30 Jun 2020 02:40:25: 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 02:40:27: 9000000 INFO @ Tue, 30 Jun 2020 02:40:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.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 02:40:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:40:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:40:32: 5000000 INFO @ Tue, 30 Jun 2020 02:40:35: 10000000 INFO @ Tue, 30 Jun 2020 02:40:35: 1000000 INFO @ Tue, 30 Jun 2020 02:40:39: 6000000 INFO @ Tue, 30 Jun 2020 02:40:42: 11000000 INFO @ Tue, 30 Jun 2020 02:40:43: 2000000 INFO @ Tue, 30 Jun 2020 02:40:46: 7000000 INFO @ Tue, 30 Jun 2020 02:40:49: 12000000 INFO @ Tue, 30 Jun 2020 02:40:49: 3000000 INFO @ Tue, 30 Jun 2020 02:40:52: 8000000 INFO @ Tue, 30 Jun 2020 02:40:56: 13000000 INFO @ Tue, 30 Jun 2020 02:40:56: 4000000 INFO @ Tue, 30 Jun 2020 02:40:59: 9000000 INFO @ Tue, 30 Jun 2020 02:41:04: 5000000 INFO @ Tue, 30 Jun 2020 02:41:04: 14000000 INFO @ Tue, 30 Jun 2020 02:41:06: 10000000 INFO @ Tue, 30 Jun 2020 02:41:11: 6000000 INFO @ Tue, 30 Jun 2020 02:41:12: 15000000 INFO @ Tue, 30 Jun 2020 02:41:13: 11000000 INFO @ Tue, 30 Jun 2020 02:41:19: 7000000 INFO @ Tue, 30 Jun 2020 02:41:19: 12000000 INFO @ Tue, 30 Jun 2020 02:41:20: 16000000 INFO @ Tue, 30 Jun 2020 02:41:20: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:41:20: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:41:20: #1 total tags in treatment: 16085704 INFO @ Tue, 30 Jun 2020 02:41:20: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:41:20: #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 02:41:21: #1 tags after filtering in treatment: 16085704 INFO @ Tue, 30 Jun 2020 02:41:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:41:21: #1 finished! INFO @ Tue, 30 Jun 2020 02:41:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:41:22: #2 number of paired peaks: 293 WARNING @ Tue, 30 Jun 2020 02:41:22: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Tue, 30 Jun 2020 02:41:22: start model_add_line... INFO @ Tue, 30 Jun 2020 02:41:22: start X-correlation... INFO @ Tue, 30 Jun 2020 02:41:22: end of X-cor INFO @ Tue, 30 Jun 2020 02:41:22: #2 finished! INFO @ Tue, 30 Jun 2020 02:41:22: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 02:41:22: #2 alternative fragment length(s) may be 3,42,549 bps INFO @ Tue, 30 Jun 2020 02:41:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.05_model.r WARNING @ Tue, 30 Jun 2020 02:41:22: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:41:22: #2 You may need to consider one of the other alternative d(s): 3,42,549 WARNING @ Tue, 30 Jun 2020 02:41:22: #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 02:41:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:41:26: 13000000 INFO @ Tue, 30 Jun 2020 02:41:26: 8000000 INFO @ Tue, 30 Jun 2020 02:41:34: 9000000 INFO @ Tue, 30 Jun 2020 02:41:34: 14000000 INFO @ Tue, 30 Jun 2020 02:41:42: 15000000 INFO @ Tue, 30 Jun 2020 02:41:42: 10000000 INFO @ Tue, 30 Jun 2020 02:41:50: 11000000 INFO @ Tue, 30 Jun 2020 02:41:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:41:50: 16000000 INFO @ Tue, 30 Jun 2020 02:41:51: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:41:51: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:41:51: #1 total tags in treatment: 16085704 INFO @ Tue, 30 Jun 2020 02:41:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:41:51: #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 02:41:52: #1 tags after filtering in treatment: 16085704 INFO @ Tue, 30 Jun 2020 02:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:41:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:41:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:41:53: #2 number of paired peaks: 293 WARNING @ Tue, 30 Jun 2020 02:41:53: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Tue, 30 Jun 2020 02:41:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:41:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:41:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:41:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:41:53: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 02:41:53: #2 alternative fragment length(s) may be 3,42,549 bps INFO @ Tue, 30 Jun 2020 02:41:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.10_model.r WARNING @ Tue, 30 Jun 2020 02:41:53: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:41:53: #2 You may need to consider one of the other alternative d(s): 3,42,549 WARNING @ Tue, 30 Jun 2020 02:41:53: #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 02:41:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:41:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:41:57: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:42:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:42:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:42:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.05_summits.bed INFO @ Tue, 30 Jun 2020 02:42:04: Done! pass1 - making usageList (522 chroms): 2 millis pass2 - checking and writing primary data (2145 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:42:05: 13000000 INFO @ Tue, 30 Jun 2020 02:42:14: 14000000 INFO @ Tue, 30 Jun 2020 02:42:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:42:22: 15000000 INFO @ Tue, 30 Jun 2020 02:42:30: 16000000 INFO @ Tue, 30 Jun 2020 02:42:31: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:42:31: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:42:31: #1 total tags in treatment: 16085704 INFO @ Tue, 30 Jun 2020 02:42:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:42:31: #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 02:42:32: #1 tags after filtering in treatment: 16085704 INFO @ Tue, 30 Jun 2020 02:42:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:42:32: #1 finished! INFO @ Tue, 30 Jun 2020 02:42:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:42:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:42:33: #2 number of paired peaks: 293 WARNING @ Tue, 30 Jun 2020 02:42:33: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Tue, 30 Jun 2020 02:42:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:42:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:42:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:42:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:42:33: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 02:42:33: #2 alternative fragment length(s) may be 3,42,549 bps INFO @ Tue, 30 Jun 2020 02:42:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.20_model.r WARNING @ Tue, 30 Jun 2020 02:42:33: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:42:33: #2 You may need to consider one of the other alternative d(s): 3,42,549 WARNING @ Tue, 30 Jun 2020 02:42:33: #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 02:42:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:42:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:42:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:42:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:42:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.10_summits.bed INFO @ Tue, 30 Jun 2020 02:42:36: Done! pass1 - making usageList (451 chroms): 1 millis pass2 - checking and writing primary data (1580 records, 4 fields): 27 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:43:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:43:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:43:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:43:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331409/SRX331409.20_summits.bed INFO @ Tue, 30 Jun 2020 02:43:15: Done! pass1 - making usageList (244 chroms): 1 millis pass2 - checking and writing primary data (509 records, 4 fields): 15 millis CompletedMACS2peakCalling