Job ID = 6454625 SRX = SRX2422629 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:23:16 prefetch.2.10.7: 1) Downloading 'SRR5110243'... 2020-06-21T09:23:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:26:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:26:05 prefetch.2.10.7: 1) 'SRR5110243' was downloaded successfully Read 19545165 spots for SRR5110243/SRR5110243.sra Written 19545165 spots for SRR5110243/SRR5110243.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: 00:06:47 19545165 reads; of these: 19545165 (100.00%) were unpaired; of these: 516717 (2.64%) aligned 0 times 13120090 (67.13%) aligned exactly 1 time 5908358 (30.23%) aligned >1 times 97.36% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 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] 2540588 / 19028448 = 0.1335 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 18:39:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.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 18:39:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:25: 1000000 INFO @ Sun, 21 Jun 2020 18:39:31: 2000000 INFO @ Sun, 21 Jun 2020 18:39:37: 3000000 INFO @ Sun, 21 Jun 2020 18:39:43: 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 18:39:48: 5000000 INFO @ Sun, 21 Jun 2020 18:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.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 18:39:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:55: 6000000 INFO @ Sun, 21 Jun 2020 18:39:57: 1000000 INFO @ Sun, 21 Jun 2020 18:40:01: 7000000 INFO @ Sun, 21 Jun 2020 18:40:04: 2000000 INFO @ Sun, 21 Jun 2020 18:40:08: 8000000 INFO @ Sun, 21 Jun 2020 18:40:12: 3000000 INFO @ Sun, 21 Jun 2020 18:40:15: 9000000 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 18:40:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.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 18:40:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:19: 4000000 INFO @ Sun, 21 Jun 2020 18:40:22: 10000000 INFO @ Sun, 21 Jun 2020 18:40:26: 1000000 INFO @ Sun, 21 Jun 2020 18:40:27: 5000000 INFO @ Sun, 21 Jun 2020 18:40:29: 11000000 INFO @ Sun, 21 Jun 2020 18:40:33: 2000000 INFO @ Sun, 21 Jun 2020 18:40:34: 6000000 INFO @ Sun, 21 Jun 2020 18:40:36: 12000000 INFO @ Sun, 21 Jun 2020 18:40:40: 3000000 INFO @ Sun, 21 Jun 2020 18:40:42: 7000000 INFO @ Sun, 21 Jun 2020 18:40:43: 13000000 INFO @ Sun, 21 Jun 2020 18:40:47: 4000000 INFO @ Sun, 21 Jun 2020 18:40:49: 8000000 INFO @ Sun, 21 Jun 2020 18:40:50: 14000000 INFO @ Sun, 21 Jun 2020 18:40:54: 5000000 INFO @ Sun, 21 Jun 2020 18:40:57: 15000000 INFO @ Sun, 21 Jun 2020 18:40:57: 9000000 INFO @ Sun, 21 Jun 2020 18:41:00: 6000000 INFO @ Sun, 21 Jun 2020 18:41:04: 16000000 INFO @ Sun, 21 Jun 2020 18:41:05: 10000000 INFO @ Sun, 21 Jun 2020 18:41:07: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:41:07: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:41:07: #1 total tags in treatment: 16487860 INFO @ Sun, 21 Jun 2020 18:41:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:07: #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 18:41:07: 7000000 INFO @ Sun, 21 Jun 2020 18:41:08: #1 tags after filtering in treatment: 16487763 INFO @ Sun, 21 Jun 2020 18:41:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:09: #2 number of paired peaks: 1420 INFO @ Sun, 21 Jun 2020 18:41:09: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:09: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:41:09: #2 alternative fragment length(s) may be 2,71,598 bps INFO @ Sun, 21 Jun 2020 18:41:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.05_model.r WARNING @ Sun, 21 Jun 2020 18:41:09: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:41:09: #2 You may need to consider one of the other alternative d(s): 2,71,598 WARNING @ Sun, 21 Jun 2020 18:41:09: #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 18:41:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:41:13: 11000000 INFO @ Sun, 21 Jun 2020 18:41:14: 8000000 INFO @ Sun, 21 Jun 2020 18:41:20: 12000000 INFO @ Sun, 21 Jun 2020 18:41:21: 9000000 INFO @ Sun, 21 Jun 2020 18:41:28: 13000000 INFO @ Sun, 21 Jun 2020 18:41:28: 10000000 INFO @ Sun, 21 Jun 2020 18:41:35: 11000000 INFO @ Sun, 21 Jun 2020 18:41:36: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:41:42: 12000000 INFO @ Sun, 21 Jun 2020 18:41:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:43: 15000000 INFO @ Sun, 21 Jun 2020 18:41:48: 13000000 INFO @ Sun, 21 Jun 2020 18:41:51: 16000000 INFO @ Sun, 21 Jun 2020 18:41:54: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:41:54: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:41:54: #1 total tags in treatment: 16487860 INFO @ Sun, 21 Jun 2020 18:41:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:54: #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 18:41:55: #1 tags after filtering in treatment: 16487763 INFO @ Sun, 21 Jun 2020 18:41:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:55: 14000000 INFO @ Sun, 21 Jun 2020 18:41:56: #2 number of paired peaks: 1420 INFO @ Sun, 21 Jun 2020 18:41:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:56: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:41:56: #2 alternative fragment length(s) may be 2,71,598 bps INFO @ Sun, 21 Jun 2020 18:41:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.10_model.r WARNING @ Sun, 21 Jun 2020 18:41:56: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:41:56: #2 You may need to consider one of the other alternative d(s): 2,71,598 WARNING @ Sun, 21 Jun 2020 18:41:56: #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 18:41:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:41:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.05_summits.bed INFO @ Sun, 21 Jun 2020 18:41:58: Done! pass1 - making usageList (613 chroms): 1 millis pass2 - checking and writing primary data (3164 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:42:01: 15000000 INFO @ Sun, 21 Jun 2020 18:42:07: 16000000 INFO @ Sun, 21 Jun 2020 18:42:10: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:42:10: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:42:10: #1 total tags in treatment: 16487860 INFO @ Sun, 21 Jun 2020 18:42:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:42:10: #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 18:42:11: #1 tags after filtering in treatment: 16487763 INFO @ Sun, 21 Jun 2020 18:42:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:42:11: #1 finished! INFO @ Sun, 21 Jun 2020 18:42:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:42:11: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:42:12: #2 number of paired peaks: 1420 INFO @ Sun, 21 Jun 2020 18:42:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:42:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:42:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:42:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:42:12: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:42:12: #2 alternative fragment length(s) may be 2,71,598 bps INFO @ Sun, 21 Jun 2020 18:42:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.20_model.r WARNING @ Sun, 21 Jun 2020 18:42:12: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:42:12: #2 You may need to consider one of the other alternative d(s): 2,71,598 WARNING @ Sun, 21 Jun 2020 18:42:12: #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 18:42:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:42:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:42:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:42:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.10_summits.bed INFO @ Sun, 21 Jun 2020 18:42:45: Done! pass1 - making usageList (502 chroms): 1 millis pass2 - checking and writing primary data (1827 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:42:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422629/SRX2422629.20_summits.bed INFO @ Sun, 21 Jun 2020 18:43:01: Done! pass1 - making usageList (329 chroms): 1 millis pass2 - checking and writing primary data (788 records, 4 fields): 11 millis CompletedMACS2peakCalling