Job ID = 6455196 SRX = SRX2831143 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:46:25 prefetch.2.10.7: 1) Downloading 'SRR5572465'... 2020-06-21T09:46:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:48:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:48:52 prefetch.2.10.7: 1) 'SRR5572465' was downloaded successfully Read 22226714 spots for SRR5572465/SRR5572465.sra Written 22226714 spots for SRR5572465/SRR5572465.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: 00:05:54 22226714 reads; of these: 22226714 (100.00%) were unpaired; of these: 1290559 (5.81%) aligned 0 times 14897506 (67.03%) aligned exactly 1 time 6038649 (27.17%) aligned >1 times 94.19% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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] 3356406 / 20936155 = 0.1603 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 19:00:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.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 19:00:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:21: 1000000 INFO @ Sun, 21 Jun 2020 19:00:26: 2000000 INFO @ Sun, 21 Jun 2020 19:00:31: 3000000 INFO @ Sun, 21 Jun 2020 19:00:36: 4000000 INFO @ Sun, 21 Jun 2020 19:00:40: 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 19:00:45: 6000000 INFO @ Sun, 21 Jun 2020 19:00:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.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 19:00:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:50: 7000000 INFO @ Sun, 21 Jun 2020 19:00:52: 1000000 INFO @ Sun, 21 Jun 2020 19:00:55: 8000000 INFO @ Sun, 21 Jun 2020 19:00:57: 2000000 INFO @ Sun, 21 Jun 2020 19:01:00: 9000000 INFO @ Sun, 21 Jun 2020 19:01:03: 3000000 INFO @ Sun, 21 Jun 2020 19:01:05: 10000000 INFO @ Sun, 21 Jun 2020 19:01:08: 4000000 INFO @ Sun, 21 Jun 2020 19:01:09: 11000000 INFO @ Sun, 21 Jun 2020 19:01:13: 5000000 INFO @ Sun, 21 Jun 2020 19:01:14: 12000000 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 19:01:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.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 19:01:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:19: 6000000 INFO @ Sun, 21 Jun 2020 19:01:19: 13000000 INFO @ Sun, 21 Jun 2020 19:01:22: 1000000 INFO @ Sun, 21 Jun 2020 19:01:24: 14000000 INFO @ Sun, 21 Jun 2020 19:01:25: 7000000 INFO @ Sun, 21 Jun 2020 19:01:27: 2000000 INFO @ Sun, 21 Jun 2020 19:01:30: 15000000 INFO @ Sun, 21 Jun 2020 19:01:30: 8000000 INFO @ Sun, 21 Jun 2020 19:01:32: 3000000 INFO @ Sun, 21 Jun 2020 19:01:35: 16000000 INFO @ Sun, 21 Jun 2020 19:01:35: 9000000 INFO @ Sun, 21 Jun 2020 19:01:37: 4000000 INFO @ Sun, 21 Jun 2020 19:01:39: 17000000 INFO @ Sun, 21 Jun 2020 19:01:41: 10000000 INFO @ Sun, 21 Jun 2020 19:01:42: 5000000 INFO @ Sun, 21 Jun 2020 19:01:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:01:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:01:43: #1 total tags in treatment: 17579749 INFO @ Sun, 21 Jun 2020 19:01:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:43: #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 19:01:43: #1 tags after filtering in treatment: 17579668 INFO @ Sun, 21 Jun 2020 19:01:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:01:44: #2 number of paired peaks: 957 WARNING @ Sun, 21 Jun 2020 19:01:44: Fewer paired peaks (957) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 957 pairs to build model! INFO @ Sun, 21 Jun 2020 19:01:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:44: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 19:01:44: #2 alternative fragment length(s) may be 2,52,577,592 bps INFO @ Sun, 21 Jun 2020 19:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.05_model.r WARNING @ Sun, 21 Jun 2020 19:01:44: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:01:44: #2 You may need to consider one of the other alternative d(s): 2,52,577,592 WARNING @ Sun, 21 Jun 2020 19:01:44: #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 19:01:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:46: 11000000 INFO @ Sun, 21 Jun 2020 19:01:47: 6000000 INFO @ Sun, 21 Jun 2020 19:01:52: 12000000 INFO @ Sun, 21 Jun 2020 19:01:52: 7000000 INFO @ Sun, 21 Jun 2020 19:01:57: 8000000 INFO @ Sun, 21 Jun 2020 19:01:57: 13000000 INFO @ Sun, 21 Jun 2020 19:02:02: 9000000 INFO @ Sun, 21 Jun 2020 19:02:03: 14000000 INFO @ Sun, 21 Jun 2020 19:02:06: 10000000 INFO @ Sun, 21 Jun 2020 19:02:09: 15000000 INFO @ Sun, 21 Jun 2020 19:02:11: 11000000 INFO @ Sun, 21 Jun 2020 19:02:14: 16000000 INFO @ Sun, 21 Jun 2020 19:02:16: 12000000 INFO @ Sun, 21 Jun 2020 19:02:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:20: 17000000 INFO @ Sun, 21 Jun 2020 19:02:21: 13000000 INFO @ Sun, 21 Jun 2020 19:02:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:02:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:02:24: #1 total tags in treatment: 17579749 INFO @ Sun, 21 Jun 2020 19:02:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:24: #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 19:02:24: #1 tags after filtering in treatment: 17579668 INFO @ Sun, 21 Jun 2020 19:02:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:25: #2 number of paired peaks: 957 WARNING @ Sun, 21 Jun 2020 19:02:25: Fewer paired peaks (957) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 957 pairs to build model! INFO @ Sun, 21 Jun 2020 19:02:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:25: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 19:02:25: #2 alternative fragment length(s) may be 2,52,577,592 bps INFO @ Sun, 21 Jun 2020 19:02:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.10_model.r WARNING @ Sun, 21 Jun 2020 19:02:25: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:02:25: #2 You may need to consider one of the other alternative d(s): 2,52,577,592 WARNING @ Sun, 21 Jun 2020 19:02:25: #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 19:02:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:26: 14000000 INFO @ Sun, 21 Jun 2020 19:02:31: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:02:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.05_summits.bed INFO @ Sun, 21 Jun 2020 19:02:33: Done! pass1 - making usageList (609 chroms): 1 millis pass2 - checking and writing primary data (3143 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:02:36: 16000000 INFO @ Sun, 21 Jun 2020 19:02:41: 17000000 INFO @ Sun, 21 Jun 2020 19:02:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:02:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:02:44: #1 total tags in treatment: 17579749 INFO @ Sun, 21 Jun 2020 19:02:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:44: #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 19:02:44: #1 tags after filtering in treatment: 17579668 INFO @ Sun, 21 Jun 2020 19:02:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:45: #2 number of paired peaks: 957 WARNING @ Sun, 21 Jun 2020 19:02:45: Fewer paired peaks (957) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 957 pairs to build model! INFO @ Sun, 21 Jun 2020 19:02:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:45: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 19:02:45: #2 alternative fragment length(s) may be 2,52,577,592 bps INFO @ Sun, 21 Jun 2020 19:02:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.20_model.r WARNING @ Sun, 21 Jun 2020 19:02:45: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:02:45: #2 You may need to consider one of the other alternative d(s): 2,52,577,592 WARNING @ Sun, 21 Jun 2020 19:02:45: #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 19:02:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:03:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.10_summits.bed INFO @ Sun, 21 Jun 2020 19:03:15: Done! pass1 - making usageList (495 chroms): 1 millis pass2 - checking and writing primary data (2032 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:03:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2831143/SRX2831143.20_summits.bed INFO @ Sun, 21 Jun 2020 19:03:35: Done! pass1 - making usageList (343 chroms): 1 millis pass2 - checking and writing primary data (955 records, 4 fields): 10 millis CompletedMACS2peakCalling