Job ID = 6453723 SRX = SRX1433366 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:38:32 prefetch.2.10.7: 1) Downloading 'SRR2919831'... 2020-06-21T08:38:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:40:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:40:09 prefetch.2.10.7: 'SRR2919831' is valid 2020-06-21T08:40:09 prefetch.2.10.7: 1) 'SRR2919831' was downloaded successfully Read 10383708 spots for SRR2919831/SRR2919831.sra Written 10383708 spots for SRR2919831/SRR2919831.sra 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: 00:02:52 10383708 reads; of these: 10383708 (100.00%) were unpaired; of these: 321417 (3.10%) aligned 0 times 7830219 (75.41%) aligned exactly 1 time 2232072 (21.50%) aligned >1 times 96.90% overall alignment rate Time searching: 00:02:52 Overall time: 00:02:52 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] 1026757 / 10062291 = 0.1020 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 @ Sun, 21 Jun 2020 17:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.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 @ Sun, 21 Jun 2020 17:46:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:14: 1000000 INFO @ Sun, 21 Jun 2020 17:46:19: 2000000 INFO @ Sun, 21 Jun 2020 17:46:25: 3000000 INFO @ Sun, 21 Jun 2020 17:46:31: 4000000 INFO @ Sun, 21 Jun 2020 17:46:36: 5000000 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 @ Sun, 21 Jun 2020 17:46:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.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 @ Sun, 21 Jun 2020 17:46:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:42: 6000000 INFO @ Sun, 21 Jun 2020 17:46:45: 1000000 INFO @ Sun, 21 Jun 2020 17:46:49: 7000000 INFO @ Sun, 21 Jun 2020 17:46:52: 2000000 INFO @ Sun, 21 Jun 2020 17:46:55: 8000000 INFO @ Sun, 21 Jun 2020 17:46:59: 3000000 INFO @ Sun, 21 Jun 2020 17:47:02: 9000000 INFO @ Sun, 21 Jun 2020 17:47:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:47:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:47:02: #1 total tags in treatment: 9035534 INFO @ Sun, 21 Jun 2020 17:47:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:47:03: #1 tags after filtering in treatment: 9035408 INFO @ Sun, 21 Jun 2020 17:47:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:03: #2 number of paired peaks: 358 WARNING @ Sun, 21 Jun 2020 17:47:03: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Sun, 21 Jun 2020 17:47:03: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:03: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:03: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:03: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:03: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 17:47:03: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 17:47:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.05_model.r WARNING @ Sun, 21 Jun 2020 17:47:03: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:47:03: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 17:47:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:47:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:06: 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 @ Sun, 21 Jun 2020 17:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.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 @ Sun, 21 Jun 2020 17:47:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:13: 5000000 INFO @ Sun, 21 Jun 2020 17:47:15: 1000000 INFO @ Sun, 21 Jun 2020 17:47:20: 6000000 INFO @ Sun, 21 Jun 2020 17:47:21: 2000000 INFO @ Sun, 21 Jun 2020 17:47:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:27: 7000000 INFO @ Sun, 21 Jun 2020 17:47:28: 3000000 INFO @ Sun, 21 Jun 2020 17:47:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.05_summits.bed INFO @ Sun, 21 Jun 2020 17:47:34: Done! pass1 - making usageList (163 chroms): 1 millis pass2 - checking and writing primary data (532 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:47:34: 4000000 INFO @ Sun, 21 Jun 2020 17:47:34: 8000000 INFO @ Sun, 21 Jun 2020 17:47:40: 5000000 INFO @ Sun, 21 Jun 2020 17:47:41: 9000000 INFO @ Sun, 21 Jun 2020 17:47:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:47:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:47:41: #1 total tags in treatment: 9035534 INFO @ Sun, 21 Jun 2020 17:47:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:47:42: #1 tags after filtering in treatment: 9035408 INFO @ Sun, 21 Jun 2020 17:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:42: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:43: #2 number of paired peaks: 358 WARNING @ Sun, 21 Jun 2020 17:47:43: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Sun, 21 Jun 2020 17:47:43: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:43: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:43: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:43: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:43: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 17:47:43: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 17:47:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.10_model.r WARNING @ Sun, 21 Jun 2020 17:47:43: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:47:43: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 17:47:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:47:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:46: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:47:52: 7000000 INFO @ Sun, 21 Jun 2020 17:47:58: 8000000 INFO @ Sun, 21 Jun 2020 17:48:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:04: 9000000 INFO @ Sun, 21 Jun 2020 17:48:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:48:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:48:04: #1 total tags in treatment: 9035534 INFO @ Sun, 21 Jun 2020 17:48:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:48:05: #1 tags after filtering in treatment: 9035408 INFO @ Sun, 21 Jun 2020 17:48:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:05: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:05: #2 number of paired peaks: 358 WARNING @ Sun, 21 Jun 2020 17:48:05: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Sun, 21 Jun 2020 17:48:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:05: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 17:48:05: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 17:48:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.20_model.r WARNING @ Sun, 21 Jun 2020 17:48:05: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:48:05: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 17:48:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:48:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:48:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.10_summits.bed INFO @ Sun, 21 Jun 2020 17:48:11: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:48:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433366/SRX1433366.20_summits.bed INFO @ Sun, 21 Jun 2020 17:48:35: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 3 millis CompletedMACS2peakCalling