Job ID = 6529310 SRX = SRX1531764 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: 00:05:45 21069300 reads; of these: 21069300 (100.00%) were unpaired; of these: 1049334 (4.98%) aligned 0 times 16002640 (75.95%) aligned exactly 1 time 4017326 (19.07%) aligned >1 times 95.02% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 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] 3088912 / 20019966 = 0.1543 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 01:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.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 01:57:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:57: 1000000 INFO @ Tue, 30 Jun 2020 01:58:03: 2000000 INFO @ Tue, 30 Jun 2020 01:58:09: 3000000 INFO @ Tue, 30 Jun 2020 01:58:16: 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 01:58:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.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 01:58:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:58:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:22: 5000000 INFO @ Tue, 30 Jun 2020 01:58:27: 1000000 INFO @ Tue, 30 Jun 2020 01:58:29: 6000000 INFO @ Tue, 30 Jun 2020 01:58:34: 2000000 INFO @ Tue, 30 Jun 2020 01:58:35: 7000000 INFO @ Tue, 30 Jun 2020 01:58:41: 3000000 INFO @ Tue, 30 Jun 2020 01:58:42: 8000000 INFO @ Tue, 30 Jun 2020 01:58:48: 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 01:58:49: 9000000 INFO @ Tue, 30 Jun 2020 01:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.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 01:58:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:58:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:55: 5000000 INFO @ Tue, 30 Jun 2020 01:58:56: 10000000 INFO @ Tue, 30 Jun 2020 01:58:58: 1000000 INFO @ Tue, 30 Jun 2020 01:59:02: 6000000 INFO @ Tue, 30 Jun 2020 01:59:03: 11000000 INFO @ Tue, 30 Jun 2020 01:59:05: 2000000 INFO @ Tue, 30 Jun 2020 01:59:09: 7000000 INFO @ Tue, 30 Jun 2020 01:59:10: 12000000 INFO @ Tue, 30 Jun 2020 01:59:13: 3000000 INFO @ Tue, 30 Jun 2020 01:59:16: 8000000 INFO @ Tue, 30 Jun 2020 01:59:17: 13000000 INFO @ Tue, 30 Jun 2020 01:59:20: 4000000 INFO @ Tue, 30 Jun 2020 01:59:23: 9000000 INFO @ Tue, 30 Jun 2020 01:59:24: 14000000 INFO @ Tue, 30 Jun 2020 01:59:27: 5000000 INFO @ Tue, 30 Jun 2020 01:59:30: 10000000 INFO @ Tue, 30 Jun 2020 01:59:31: 15000000 INFO @ Tue, 30 Jun 2020 01:59:34: 6000000 INFO @ Tue, 30 Jun 2020 01:59:36: 11000000 INFO @ Tue, 30 Jun 2020 01:59:38: 16000000 INFO @ Tue, 30 Jun 2020 01:59:41: 7000000 INFO @ Tue, 30 Jun 2020 01:59:43: 12000000 INFO @ Tue, 30 Jun 2020 01:59:45: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:59:45: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:59:45: #1 total tags in treatment: 16931054 INFO @ Tue, 30 Jun 2020 01:59:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:59:45: #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 01:59:46: #1 tags after filtering in treatment: 16931052 INFO @ Tue, 30 Jun 2020 01:59:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:59:46: #1 finished! INFO @ Tue, 30 Jun 2020 01:59:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:59:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:59:47: #2 number of paired peaks: 484 WARNING @ Tue, 30 Jun 2020 01:59:47: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Tue, 30 Jun 2020 01:59:47: start model_add_line... INFO @ Tue, 30 Jun 2020 01:59:47: start X-correlation... INFO @ Tue, 30 Jun 2020 01:59:47: end of X-cor INFO @ Tue, 30 Jun 2020 01:59:47: #2 finished! INFO @ Tue, 30 Jun 2020 01:59:47: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 01:59:47: #2 alternative fragment length(s) may be 2,36 bps INFO @ Tue, 30 Jun 2020 01:59:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.05_model.r WARNING @ Tue, 30 Jun 2020 01:59:47: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:59:47: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Tue, 30 Jun 2020 01:59:47: #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 01:59:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:59:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:59:48: 8000000 INFO @ Tue, 30 Jun 2020 01:59:50: 13000000 INFO @ Tue, 30 Jun 2020 01:59:55: 9000000 INFO @ Tue, 30 Jun 2020 01:59:58: 14000000 INFO @ Tue, 30 Jun 2020 02:00:02: 10000000 INFO @ Tue, 30 Jun 2020 02:00:05: 15000000 INFO @ Tue, 30 Jun 2020 02:00:09: 11000000 INFO @ Tue, 30 Jun 2020 02:00:12: 16000000 INFO @ Tue, 30 Jun 2020 02:00:16: 12000000 INFO @ Tue, 30 Jun 2020 02:00:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:00:19: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:00:19: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:00:19: #1 total tags in treatment: 16931054 INFO @ Tue, 30 Jun 2020 02:00:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:00:19: #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 02:00:20: #1 tags after filtering in treatment: 16931052 INFO @ Tue, 30 Jun 2020 02:00:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:00:20: #1 finished! INFO @ Tue, 30 Jun 2020 02:00:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:00:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:00:21: #2 number of paired peaks: 484 WARNING @ Tue, 30 Jun 2020 02:00:21: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Tue, 30 Jun 2020 02:00:21: start model_add_line... INFO @ Tue, 30 Jun 2020 02:00:22: start X-correlation... INFO @ Tue, 30 Jun 2020 02:00:22: end of X-cor INFO @ Tue, 30 Jun 2020 02:00:22: #2 finished! INFO @ Tue, 30 Jun 2020 02:00:22: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 02:00:22: #2 alternative fragment length(s) may be 2,36 bps INFO @ Tue, 30 Jun 2020 02:00:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.10_model.r WARNING @ Tue, 30 Jun 2020 02:00:22: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:00:22: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Tue, 30 Jun 2020 02:00:22: #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 02:00:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:00:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:00:23: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:00:30: 14000000 INFO @ Tue, 30 Jun 2020 02:00:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:00:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.05_summits.bed INFO @ Tue, 30 Jun 2020 02:00:34: Done! pass1 - making usageList (558 chroms): 1 millis pass2 - checking and writing primary data (2314 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:00:37: 15000000 INFO @ Tue, 30 Jun 2020 02:00:44: 16000000 INFO @ Tue, 30 Jun 2020 02:00:51: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:00:51: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:00:51: #1 total tags in treatment: 16931054 INFO @ Tue, 30 Jun 2020 02:00:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:00:51: #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 02:00:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:00:52: #1 tags after filtering in treatment: 16931052 INFO @ Tue, 30 Jun 2020 02:00:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:00:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:00:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:00:53: #2 number of paired peaks: 484 WARNING @ Tue, 30 Jun 2020 02:00:53: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Tue, 30 Jun 2020 02:00:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:00:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:00:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:00:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:00:53: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 02:00:53: #2 alternative fragment length(s) may be 2,36 bps INFO @ Tue, 30 Jun 2020 02:00:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.20_model.r WARNING @ Tue, 30 Jun 2020 02:00:53: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:00:53: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Tue, 30 Jun 2020 02:00:53: #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 02:00:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:00:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.10_summits.bed INFO @ Tue, 30 Jun 2020 02:01:08: Done! pass1 - making usageList (452 chroms): 1 millis pass2 - checking and writing primary data (1735 records, 4 fields): 27 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:01:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:01:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:01:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:01:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1531764/SRX1531764.20_summits.bed INFO @ Tue, 30 Jun 2020 02:01:39: Done! pass1 - making usageList (265 chroms): 2 millis pass2 - checking and writing primary data (527 records, 4 fields): 15 millis CompletedMACS2peakCalling