Job ID = 6458624 SRX = SRX5343155 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:39:26 prefetch.2.10.7: 1) Downloading 'SRR8540855'... 2020-06-21T12:39:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:41:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:41:50 prefetch.2.10.7: 1) 'SRR8540855' was downloaded successfully 2020-06-21T12:41:50 prefetch.2.10.7: 'SRR8540855' has 0 unresolved dependencies Read 19990720 spots for SRR8540855/SRR8540855.sra Written 19990720 spots for SRR8540855/SRR8540855.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: 00:05:51 19990720 reads; of these: 19990720 (100.00%) were unpaired; of these: 1778151 (8.89%) aligned 0 times 14430793 (72.19%) aligned exactly 1 time 3781776 (18.92%) aligned >1 times 91.11% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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] 7816883 / 18212569 = 0.4292 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 21:53:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.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 21:53:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:28: 1000000 INFO @ Sun, 21 Jun 2020 21:53:35: 2000000 INFO @ Sun, 21 Jun 2020 21:53:41: 3000000 INFO @ Sun, 21 Jun 2020 21:53:48: 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 @ Sun, 21 Jun 2020 21:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.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 21:53:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:54: 5000000 INFO @ Sun, 21 Jun 2020 21:53:58: 1000000 INFO @ Sun, 21 Jun 2020 21:54:01: 6000000 INFO @ Sun, 21 Jun 2020 21:54:05: 2000000 INFO @ Sun, 21 Jun 2020 21:54:08: 7000000 INFO @ Sun, 21 Jun 2020 21:54:12: 3000000 INFO @ Sun, 21 Jun 2020 21:54:15: 8000000 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 21:54:19: 4000000 INFO @ Sun, 21 Jun 2020 21:54:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.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 21:54:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:23: 9000000 INFO @ Sun, 21 Jun 2020 21:54:26: 5000000 INFO @ Sun, 21 Jun 2020 21:54:28: 1000000 INFO @ Sun, 21 Jun 2020 21:54:30: 10000000 INFO @ Sun, 21 Jun 2020 21:54:33: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:54:33: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:54:33: #1 total tags in treatment: 10395686 INFO @ Sun, 21 Jun 2020 21:54:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:33: #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 21:54:33: #1 tags after filtering in treatment: 10395686 INFO @ Sun, 21 Jun 2020 21:54:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:34: 6000000 INFO @ Sun, 21 Jun 2020 21:54:34: #2 number of paired peaks: 682 WARNING @ Sun, 21 Jun 2020 21:54:34: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Sun, 21 Jun 2020 21:54:34: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:34: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:34: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:34: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:34: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 21:54:34: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 21 Jun 2020 21:54:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.05_model.r WARNING @ Sun, 21 Jun 2020 21:54:34: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:34: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 21 Jun 2020 21:54:34: #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 21:54:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:34: 2000000 INFO @ Sun, 21 Jun 2020 21:54:40: 3000000 INFO @ Sun, 21 Jun 2020 21:54:41: 7000000 INFO @ Sun, 21 Jun 2020 21:54:47: 4000000 INFO @ Sun, 21 Jun 2020 21:54:48: 8000000 INFO @ Sun, 21 Jun 2020 21:54:53: 5000000 INFO @ Sun, 21 Jun 2020 21:54:55: 9000000 INFO @ Sun, 21 Jun 2020 21:54:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:00: 6000000 INFO @ Sun, 21 Jun 2020 21:55:02: 10000000 INFO @ Sun, 21 Jun 2020 21:55:05: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:55:05: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:55:05: #1 total tags in treatment: 10395686 INFO @ Sun, 21 Jun 2020 21:55:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:05: #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 21:55:06: #1 tags after filtering in treatment: 10395686 INFO @ Sun, 21 Jun 2020 21:55:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:06: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.05_summits.bed INFO @ Sun, 21 Jun 2020 21:55:06: Done! INFO @ Sun, 21 Jun 2020 21:55:06: 7000000 pass1 - making usageList (587 chroms): 1 millis pass2 - checking and writing primary data (4265 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:55:06: #2 number of paired peaks: 682 WARNING @ Sun, 21 Jun 2020 21:55:06: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:06: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:06: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:06: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:06: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:06: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 21:55:06: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 21 Jun 2020 21:55:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.10_model.r WARNING @ Sun, 21 Jun 2020 21:55:06: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:06: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 21 Jun 2020 21:55:06: #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 21:55:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:06: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:55:12: 8000000 INFO @ Sun, 21 Jun 2020 21:55:17: 9000000 INFO @ Sun, 21 Jun 2020 21:55:23: 10000000 INFO @ Sun, 21 Jun 2020 21:55:25: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:55:25: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:55:25: #1 total tags in treatment: 10395686 INFO @ Sun, 21 Jun 2020 21:55:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:25: #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 21:55:26: #1 tags after filtering in treatment: 10395686 INFO @ Sun, 21 Jun 2020 21:55:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:26: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:26: #2 number of paired peaks: 682 WARNING @ Sun, 21 Jun 2020 21:55:26: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:27: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 21:55:27: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 21 Jun 2020 21:55:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.20_model.r WARNING @ Sun, 21 Jun 2020 21:55:27: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:27: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 21 Jun 2020 21:55:27: #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 21:55:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:55:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.10_summits.bed INFO @ Sun, 21 Jun 2020 21:55:38: Done! pass1 - making usageList (348 chroms): 1 millis pass2 - checking and writing primary data (997 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:55:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343155/SRX5343155.20_summits.bed INFO @ Sun, 21 Jun 2020 21:56:00: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (296 records, 4 fields): 5 millis CompletedMACS2peakCalling