Job ID = 6454630 SRX = SRX2422634 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:30:29 prefetch.2.10.7: 1) Downloading 'SRR5110248'... 2020-06-21T09:30:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:16 prefetch.2.10.7: 'SRR5110248' is valid 2020-06-21T09:33:16 prefetch.2.10.7: 1) 'SRR5110248' was downloaded successfully Read 14574177 spots for SRR5110248/SRR5110248.sra Written 14574177 spots for SRR5110248/SRR5110248.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: 00:05:00 14574177 reads; of these: 14574177 (100.00%) were unpaired; of these: 590350 (4.05%) aligned 0 times 9724081 (66.72%) aligned exactly 1 time 4259746 (29.23%) aligned >1 times 95.95% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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] 1893710 / 13983827 = 0.1354 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 18:43:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.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 18:43:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:26: 1000000 INFO @ Sun, 21 Jun 2020 18:43:34: 2000000 INFO @ Sun, 21 Jun 2020 18:43:42: 3000000 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 18:43:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.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 18:43:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:49: 4000000 INFO @ Sun, 21 Jun 2020 18:43:57: 1000000 INFO @ Sun, 21 Jun 2020 18:43:58: 5000000 INFO @ Sun, 21 Jun 2020 18:44:05: 2000000 INFO @ Sun, 21 Jun 2020 18:44:06: 6000000 INFO @ Sun, 21 Jun 2020 18:44:14: 3000000 INFO @ Sun, 21 Jun 2020 18:44:15: 7000000 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 18:44:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.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 18:44:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:22: 4000000 INFO @ Sun, 21 Jun 2020 18:44:23: 8000000 INFO @ Sun, 21 Jun 2020 18:44:28: 1000000 INFO @ Sun, 21 Jun 2020 18:44:31: 5000000 INFO @ Sun, 21 Jun 2020 18:44:32: 9000000 INFO @ Sun, 21 Jun 2020 18:44:37: 2000000 INFO @ Sun, 21 Jun 2020 18:44:40: 6000000 INFO @ Sun, 21 Jun 2020 18:44:40: 10000000 INFO @ Sun, 21 Jun 2020 18:44:46: 3000000 INFO @ Sun, 21 Jun 2020 18:44:49: 7000000 INFO @ Sun, 21 Jun 2020 18:44:49: 11000000 INFO @ Sun, 21 Jun 2020 18:44:55: 4000000 INFO @ Sun, 21 Jun 2020 18:44:58: 8000000 INFO @ Sun, 21 Jun 2020 18:44:58: 12000000 INFO @ Sun, 21 Jun 2020 18:44:59: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:44:59: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:44:59: #1 total tags in treatment: 12090117 INFO @ Sun, 21 Jun 2020 18:44:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:59: #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 18:44:59: #1 tags after filtering in treatment: 12090006 INFO @ Sun, 21 Jun 2020 18:44:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:00: #2 number of paired peaks: 1525 INFO @ Sun, 21 Jun 2020 18:45:00: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:00: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:00: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:00: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:00: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 18:45:00: #2 alternative fragment length(s) may be 3,80,583,586 bps INFO @ Sun, 21 Jun 2020 18:45:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.05_model.r WARNING @ Sun, 21 Jun 2020 18:45:00: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:00: #2 You may need to consider one of the other alternative d(s): 3,80,583,586 WARNING @ Sun, 21 Jun 2020 18:45:00: #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 18:45:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:03: 5000000 INFO @ Sun, 21 Jun 2020 18:45:06: 9000000 INFO @ Sun, 21 Jun 2020 18:45:12: 6000000 INFO @ Sun, 21 Jun 2020 18:45:15: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:45:21: 7000000 INFO @ Sun, 21 Jun 2020 18:45:24: 11000000 INFO @ Sun, 21 Jun 2020 18:45:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:29: 8000000 INFO @ Sun, 21 Jun 2020 18:45:32: 12000000 INFO @ Sun, 21 Jun 2020 18:45:33: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:45:33: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:45:33: #1 total tags in treatment: 12090117 INFO @ Sun, 21 Jun 2020 18:45:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:33: #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 18:45:34: #1 tags after filtering in treatment: 12090006 INFO @ Sun, 21 Jun 2020 18:45:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:34: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:34: #2 number of paired peaks: 1525 INFO @ Sun, 21 Jun 2020 18:45:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:35: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 18:45:35: #2 alternative fragment length(s) may be 3,80,583,586 bps INFO @ Sun, 21 Jun 2020 18:45:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.10_model.r WARNING @ Sun, 21 Jun 2020 18:45:35: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:35: #2 You may need to consider one of the other alternative d(s): 3,80,583,586 WARNING @ Sun, 21 Jun 2020 18:45:35: #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 18:45:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:38: 9000000 INFO @ Sun, 21 Jun 2020 18:45:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.05_summits.bed INFO @ Sun, 21 Jun 2020 18:45:41: Done! pass1 - making usageList (624 chroms): 2 millis pass2 - checking and writing primary data (3041 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:45:46: 10000000 INFO @ Sun, 21 Jun 2020 18:45:54: 11000000 INFO @ Sun, 21 Jun 2020 18:46:02: 12000000 INFO @ Sun, 21 Jun 2020 18:46:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:03: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:46:03: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:46:03: #1 total tags in treatment: 12090117 INFO @ Sun, 21 Jun 2020 18:46:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:03: #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 18:46:03: #1 tags after filtering in treatment: 12090006 INFO @ Sun, 21 Jun 2020 18:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:03: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:04: #2 number of paired peaks: 1525 INFO @ Sun, 21 Jun 2020 18:46:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:04: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 18:46:04: #2 alternative fragment length(s) may be 3,80,583,586 bps INFO @ Sun, 21 Jun 2020 18:46:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.20_model.r WARNING @ Sun, 21 Jun 2020 18:46:04: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:46:04: #2 You may need to consider one of the other alternative d(s): 3,80,583,586 WARNING @ Sun, 21 Jun 2020 18:46:04: #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 18:46:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.10_summits.bed INFO @ Sun, 21 Jun 2020 18:46:16: Done! pass1 - making usageList (470 chroms): 1 millis pass2 - checking and writing primary data (1645 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422634/SRX2422634.20_summits.bed INFO @ Sun, 21 Jun 2020 18:46:43: Done! pass1 - making usageList (294 chroms): 1 millis pass2 - checking and writing primary data (650 records, 4 fields): 11 millis CompletedMACS2peakCalling