Job ID = 6454431 SRX = SRX2055959 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:20:24 prefetch.2.10.7: 1) Downloading 'SRR4069191'... 2020-06-21T09:20:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:22:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:22:11 prefetch.2.10.7: 'SRR4069191' is valid 2020-06-21T09:22:11 prefetch.2.10.7: 1) 'SRR4069191' was downloaded successfully Read 16887197 spots for SRR4069191/SRR4069191.sra Written 16887197 spots for SRR4069191/SRR4069191.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: 00:00:01 Multiseed full-index search: 00:05:58 16887197 reads; of these: 16887197 (100.00%) were unpaired; of these: 736484 (4.36%) aligned 0 times 10529793 (62.35%) aligned exactly 1 time 5620920 (33.29%) aligned >1 times 95.64% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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] 2305376 / 16150713 = 0.1427 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 18:32:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.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 18:32:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:47: 1000000 INFO @ Sun, 21 Jun 2020 18:32:52: 2000000 INFO @ Sun, 21 Jun 2020 18:32:57: 3000000 INFO @ Sun, 21 Jun 2020 18:33:02: 4000000 INFO @ Sun, 21 Jun 2020 18:33:07: 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 18:33:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.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 18:33:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:12: 6000000 INFO @ Sun, 21 Jun 2020 18:33:17: 1000000 INFO @ Sun, 21 Jun 2020 18:33:18: 7000000 INFO @ Sun, 21 Jun 2020 18:33:22: 2000000 INFO @ Sun, 21 Jun 2020 18:33:23: 8000000 INFO @ Sun, 21 Jun 2020 18:33:28: 3000000 INFO @ Sun, 21 Jun 2020 18:33:28: 9000000 INFO @ Sun, 21 Jun 2020 18:33:33: 4000000 INFO @ Sun, 21 Jun 2020 18:33:33: 10000000 INFO @ Sun, 21 Jun 2020 18:33:38: 5000000 INFO @ Sun, 21 Jun 2020 18:33:38: 11000000 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 18:33:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.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 18:33:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:43: 6000000 INFO @ Sun, 21 Jun 2020 18:33:44: 12000000 INFO @ Sun, 21 Jun 2020 18:33:47: 1000000 INFO @ Sun, 21 Jun 2020 18:33:49: 7000000 INFO @ Sun, 21 Jun 2020 18:33:49: 13000000 INFO @ Sun, 21 Jun 2020 18:33:53: 2000000 INFO @ Sun, 21 Jun 2020 18:33:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:54: #1 total tags in treatment: 13845337 INFO @ Sun, 21 Jun 2020 18:33:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:54: #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 18:33:54: #1 tags after filtering in treatment: 13845255 INFO @ Sun, 21 Jun 2020 18:33:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:55: 8000000 INFO @ Sun, 21 Jun 2020 18:33:55: #2 number of paired peaks: 1901 INFO @ Sun, 21 Jun 2020 18:33:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:56: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 18:33:56: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 18:33:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.05_model.r WARNING @ Sun, 21 Jun 2020 18:33:56: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:56: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 18:33:56: #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 18:33:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:58: 3000000 INFO @ Sun, 21 Jun 2020 18:34:00: 9000000 INFO @ Sun, 21 Jun 2020 18:34:03: 4000000 INFO @ Sun, 21 Jun 2020 18:34:05: 10000000 INFO @ Sun, 21 Jun 2020 18:34:09: 5000000 INFO @ Sun, 21 Jun 2020 18:34:11: 11000000 INFO @ Sun, 21 Jun 2020 18:34:14: 6000000 INFO @ Sun, 21 Jun 2020 18:34:16: 12000000 INFO @ Sun, 21 Jun 2020 18:34:20: 7000000 INFO @ Sun, 21 Jun 2020 18:34:22: 13000000 INFO @ Sun, 21 Jun 2020 18:34:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:25: 8000000 INFO @ Sun, 21 Jun 2020 18:34:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:34:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:34:27: #1 total tags in treatment: 13845337 INFO @ Sun, 21 Jun 2020 18:34:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:27: #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 18:34:27: #1 tags after filtering in treatment: 13845255 INFO @ Sun, 21 Jun 2020 18:34:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:28: #2 number of paired peaks: 1901 INFO @ Sun, 21 Jun 2020 18:34:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:28: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 18:34:28: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 18:34:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.10_model.r WARNING @ Sun, 21 Jun 2020 18:34:28: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:34:28: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 18:34:28: #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 18:34:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:31: 9000000 INFO @ Sun, 21 Jun 2020 18:34:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.05_summits.bed INFO @ Sun, 21 Jun 2020 18:34:36: Done! INFO @ Sun, 21 Jun 2020 18:34:36: 10000000 pass1 - making usageList (656 chroms): 1 millis pass2 - checking and writing primary data (3016 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:34:42: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:34:47: 12000000 INFO @ Sun, 21 Jun 2020 18:34:53: 13000000 INFO @ Sun, 21 Jun 2020 18:34:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:34:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:34:58: #1 total tags in treatment: 13845337 INFO @ Sun, 21 Jun 2020 18:34:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:58: #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 18:34:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:58: #1 tags after filtering in treatment: 13845255 INFO @ Sun, 21 Jun 2020 18:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:59: #2 number of paired peaks: 1901 INFO @ Sun, 21 Jun 2020 18:34:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:59: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 18:34:59: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 18:34:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.20_model.r WARNING @ Sun, 21 Jun 2020 18:34:59: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:34:59: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 18:34:59: #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 18:34:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.10_summits.bed INFO @ Sun, 21 Jun 2020 18:35:12: Done! pass1 - making usageList (528 chroms): 1 millis pass2 - checking and writing primary data (2132 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:35:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055959/SRX2055959.20_summits.bed INFO @ Sun, 21 Jun 2020 18:35:41: Done! pass1 - making usageList (394 chroms): 1 millis pass2 - checking and writing primary data (1108 records, 4 fields): 14 millis CompletedMACS2peakCalling