Job ID = 6453108 SRX = SRX1032407 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:23:02 prefetch.2.10.7: 1) Downloading 'SRR2031908'... 2020-06-21T08:23:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:19 prefetch.2.10.7: 'SRR2031908' is valid 2020-06-21T08:27:19 prefetch.2.10.7: 1) 'SRR2031908' was downloaded successfully Read 18955656 spots for SRR2031908/SRR2031908.sra Written 18955656 spots for SRR2031908/SRR2031908.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:53 18955656 reads; of these: 18955656 (100.00%) were unpaired; of these: 1440678 (7.60%) aligned 0 times 11566928 (61.02%) aligned exactly 1 time 5948050 (31.38%) aligned >1 times 92.40% 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 8 files... [bam_rmdupse_core] 2894098 / 17514978 = 0.1652 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 17:39:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.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 17:39:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:39:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:40:08: 1000000 INFO @ Sun, 21 Jun 2020 17:40:16: 2000000 INFO @ Sun, 21 Jun 2020 17:40:25: 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 17:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.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 17:40:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:40:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:40:33: 4000000 INFO @ Sun, 21 Jun 2020 17:40:38: 1000000 INFO @ Sun, 21 Jun 2020 17:40:42: 5000000 INFO @ Sun, 21 Jun 2020 17:40:47: 2000000 INFO @ Sun, 21 Jun 2020 17:40:50: 6000000 INFO @ Sun, 21 Jun 2020 17:40:55: 3000000 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 17:40:59: 7000000 INFO @ Sun, 21 Jun 2020 17:40:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.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 17:40:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:40:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:41:04: 4000000 INFO @ Sun, 21 Jun 2020 17:41:08: 1000000 INFO @ Sun, 21 Jun 2020 17:41:08: 8000000 INFO @ Sun, 21 Jun 2020 17:41:13: 5000000 INFO @ Sun, 21 Jun 2020 17:41:16: 2000000 INFO @ Sun, 21 Jun 2020 17:41:17: 9000000 INFO @ Sun, 21 Jun 2020 17:41:22: 6000000 INFO @ Sun, 21 Jun 2020 17:41:25: 3000000 INFO @ Sun, 21 Jun 2020 17:41:26: 10000000 INFO @ Sun, 21 Jun 2020 17:41:31: 7000000 INFO @ Sun, 21 Jun 2020 17:41:33: 4000000 INFO @ Sun, 21 Jun 2020 17:41:35: 11000000 INFO @ Sun, 21 Jun 2020 17:41:39: 8000000 INFO @ Sun, 21 Jun 2020 17:41:42: 5000000 INFO @ Sun, 21 Jun 2020 17:41:45: 12000000 INFO @ Sun, 21 Jun 2020 17:41:48: 9000000 INFO @ Sun, 21 Jun 2020 17:41:50: 6000000 INFO @ Sun, 21 Jun 2020 17:41:55: 13000000 INFO @ Sun, 21 Jun 2020 17:41:56: 10000000 INFO @ Sun, 21 Jun 2020 17:41:58: 7000000 INFO @ Sun, 21 Jun 2020 17:42:05: 11000000 INFO @ Sun, 21 Jun 2020 17:42:06: 8000000 INFO @ Sun, 21 Jun 2020 17:42:07: 14000000 INFO @ Sun, 21 Jun 2020 17:42:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:42:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:42:12: #1 total tags in treatment: 14620880 INFO @ Sun, 21 Jun 2020 17:42:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:42:12: #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 17:42:14: #1 tags after filtering in treatment: 14620880 INFO @ Sun, 21 Jun 2020 17:42:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:42:14: #1 finished! INFO @ Sun, 21 Jun 2020 17:42:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:42:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:42:14: 12000000 INFO @ Sun, 21 Jun 2020 17:42:14: 9000000 INFO @ Sun, 21 Jun 2020 17:42:15: #2 number of paired peaks: 991 WARNING @ Sun, 21 Jun 2020 17:42:15: Fewer paired peaks (991) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 991 pairs to build model! INFO @ Sun, 21 Jun 2020 17:42:15: start model_add_line... INFO @ Sun, 21 Jun 2020 17:42:15: start X-correlation... INFO @ Sun, 21 Jun 2020 17:42:15: end of X-cor INFO @ Sun, 21 Jun 2020 17:42:15: #2 finished! INFO @ Sun, 21 Jun 2020 17:42:15: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 17:42:15: #2 alternative fragment length(s) may be 4,54,557 bps INFO @ Sun, 21 Jun 2020 17:42:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.05_model.r WARNING @ Sun, 21 Jun 2020 17:42:15: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:42:15: #2 You may need to consider one of the other alternative d(s): 4,54,557 WARNING @ Sun, 21 Jun 2020 17:42:15: #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 17:42:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:42:15: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:42:22: 10000000 INFO @ Sun, 21 Jun 2020 17:42:22: 13000000 INFO @ Sun, 21 Jun 2020 17:42:29: 11000000 INFO @ Sun, 21 Jun 2020 17:42:30: 14000000 INFO @ Sun, 21 Jun 2020 17:42:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:42:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:42:36: #1 total tags in treatment: 14620880 INFO @ Sun, 21 Jun 2020 17:42:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:42:36: #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 17:42:37: #1 tags after filtering in treatment: 14620880 INFO @ Sun, 21 Jun 2020 17:42:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:42:37: #1 finished! INFO @ Sun, 21 Jun 2020 17:42:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:42:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:42:38: #2 number of paired peaks: 991 WARNING @ Sun, 21 Jun 2020 17:42:38: Fewer paired peaks (991) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 991 pairs to build model! INFO @ Sun, 21 Jun 2020 17:42:38: start model_add_line... INFO @ Sun, 21 Jun 2020 17:42:38: start X-correlation... INFO @ Sun, 21 Jun 2020 17:42:38: end of X-cor INFO @ Sun, 21 Jun 2020 17:42:38: #2 finished! INFO @ Sun, 21 Jun 2020 17:42:38: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 17:42:38: #2 alternative fragment length(s) may be 4,54,557 bps INFO @ Sun, 21 Jun 2020 17:42:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.10_model.r WARNING @ Sun, 21 Jun 2020 17:42:38: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:42:38: #2 You may need to consider one of the other alternative d(s): 4,54,557 WARNING @ Sun, 21 Jun 2020 17:42:38: #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 17:42:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:42:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:42:38: 12000000 INFO @ Sun, 21 Jun 2020 17:42:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:42:46: 13000000 INFO @ Sun, 21 Jun 2020 17:42:54: 14000000 INFO @ Sun, 21 Jun 2020 17:42:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:42:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:42:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.05_summits.bed INFO @ Sun, 21 Jun 2020 17:42:55: Done! pass1 - making usageList (801 chroms): 2 millis pass2 - checking and writing primary data (3505 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:42:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:42:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:42:58: #1 total tags in treatment: 14620880 INFO @ Sun, 21 Jun 2020 17:42:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:42:58: #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 17:42:59: #1 tags after filtering in treatment: 14620880 INFO @ Sun, 21 Jun 2020 17:42:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:42:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:42:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:42:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:43:00: #2 number of paired peaks: 991 WARNING @ Sun, 21 Jun 2020 17:43:00: Fewer paired peaks (991) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 991 pairs to build model! INFO @ Sun, 21 Jun 2020 17:43:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:43:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:43:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:43:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:43:00: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 17:43:00: #2 alternative fragment length(s) may be 4,54,557 bps INFO @ Sun, 21 Jun 2020 17:43:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.20_model.r WARNING @ Sun, 21 Jun 2020 17:43:00: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:43:00: #2 You may need to consider one of the other alternative d(s): 4,54,557 WARNING @ Sun, 21 Jun 2020 17:43:00: #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 17:43:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:43:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:43:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:43:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:43:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:43:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.10_summits.bed INFO @ Sun, 21 Jun 2020 17:43:19: Done! pass1 - making usageList (646 chroms): 2 millis pass2 - checking and writing primary data (2587 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:43:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:43:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:43:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:43:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032407/SRX1032407.20_summits.bed INFO @ Sun, 21 Jun 2020 17:43:40: Done! pass1 - making usageList (491 chroms): 1 millis pass2 - checking and writing primary data (1319 records, 4 fields): 28 millis CompletedMACS2peakCalling