Job ID = 6508487 SRX = SRX287909 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:23:59 prefetch.2.10.7: 1) Downloading 'SRR870098'... 2020-06-26T14:23:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:28:55 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:28:55 prefetch.2.10.7: 1) 'SRR870098' was downloaded successfully Read 19930693 spots for SRR870098/SRR870098.sra Written 19930693 spots for SRR870098/SRR870098.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: 00:06:01 19930693 reads; of these: 19930693 (100.00%) were unpaired; of these: 1532840 (7.69%) aligned 0 times 13016013 (65.31%) aligned exactly 1 time 5381840 (27.00%) aligned >1 times 92.31% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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] 2759889 / 18397853 = 0.1500 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 @ Fri, 26 Jun 2020 23:40:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.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 @ Fri, 26 Jun 2020 23:40:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:40:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:41:04: 1000000 INFO @ Fri, 26 Jun 2020 23:41:11: 2000000 INFO @ Fri, 26 Jun 2020 23:41:17: 3000000 INFO @ Fri, 26 Jun 2020 23:41:23: 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 @ Fri, 26 Jun 2020 23:41:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.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 @ Fri, 26 Jun 2020 23:41:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:41:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:41:29: 5000000 INFO @ Fri, 26 Jun 2020 23:41:35: 1000000 INFO @ Fri, 26 Jun 2020 23:41:36: 6000000 INFO @ Fri, 26 Jun 2020 23:41:42: 2000000 INFO @ Fri, 26 Jun 2020 23:41:42: 7000000 INFO @ Fri, 26 Jun 2020 23:41:48: 3000000 INFO @ Fri, 26 Jun 2020 23:41:49: 8000000 INFO @ Fri, 26 Jun 2020 23:41:55: 4000000 INFO @ Fri, 26 Jun 2020 23:41:55: 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 @ Fri, 26 Jun 2020 23:41:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.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 @ Fri, 26 Jun 2020 23:41:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:41:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:42:02: 5000000 INFO @ Fri, 26 Jun 2020 23:42:02: 10000000 INFO @ Fri, 26 Jun 2020 23:42:06: 1000000 INFO @ Fri, 26 Jun 2020 23:42:09: 6000000 INFO @ Fri, 26 Jun 2020 23:42:09: 11000000 INFO @ Fri, 26 Jun 2020 23:42:14: 2000000 INFO @ Fri, 26 Jun 2020 23:42:16: 7000000 INFO @ Fri, 26 Jun 2020 23:42:17: 12000000 INFO @ Fri, 26 Jun 2020 23:42:22: 3000000 INFO @ Fri, 26 Jun 2020 23:42:23: 8000000 INFO @ Fri, 26 Jun 2020 23:42:24: 13000000 INFO @ Fri, 26 Jun 2020 23:42:30: 9000000 INFO @ Fri, 26 Jun 2020 23:42:30: 4000000 INFO @ Fri, 26 Jun 2020 23:42:31: 14000000 INFO @ Fri, 26 Jun 2020 23:42:37: 10000000 INFO @ Fri, 26 Jun 2020 23:42:38: 5000000 INFO @ Fri, 26 Jun 2020 23:42:39: 15000000 INFO @ Fri, 26 Jun 2020 23:42:43: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:42:43: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:42:43: #1 total tags in treatment: 15637964 INFO @ Fri, 26 Jun 2020 23:42:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:42:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:42:44: #1 tags after filtering in treatment: 15637964 INFO @ Fri, 26 Jun 2020 23:42:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:42:44: #1 finished! INFO @ Fri, 26 Jun 2020 23:42:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:42:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:42:44: 11000000 INFO @ Fri, 26 Jun 2020 23:42:45: #2 number of paired peaks: 353 WARNING @ Fri, 26 Jun 2020 23:42:45: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Fri, 26 Jun 2020 23:42:45: start model_add_line... INFO @ Fri, 26 Jun 2020 23:42:45: start X-correlation... INFO @ Fri, 26 Jun 2020 23:42:45: end of X-cor INFO @ Fri, 26 Jun 2020 23:42:45: #2 finished! INFO @ Fri, 26 Jun 2020 23:42:45: #2 predicted fragment length is 33 bps INFO @ Fri, 26 Jun 2020 23:42:45: #2 alternative fragment length(s) may be 3,33 bps INFO @ Fri, 26 Jun 2020 23:42:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.05_model.r WARNING @ Fri, 26 Jun 2020 23:42:45: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:42:45: #2 You may need to consider one of the other alternative d(s): 3,33 WARNING @ Fri, 26 Jun 2020 23:42:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:42:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:42:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:42:46: 6000000 INFO @ Fri, 26 Jun 2020 23:42:51: 12000000 INFO @ Fri, 26 Jun 2020 23:42:54: 7000000 INFO @ Fri, 26 Jun 2020 23:42:58: 13000000 INFO @ Fri, 26 Jun 2020 23:43:02: 8000000 INFO @ Fri, 26 Jun 2020 23:43:05: 14000000 INFO @ Fri, 26 Jun 2020 23:43:09: 9000000 INFO @ Fri, 26 Jun 2020 23:43:12: 15000000 INFO @ Fri, 26 Jun 2020 23:43:17: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:43:17: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:43:17: #1 total tags in treatment: 15637964 INFO @ Fri, 26 Jun 2020 23:43:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:43:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:43:17: 10000000 INFO @ Fri, 26 Jun 2020 23:43:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:43:17: #1 tags after filtering in treatment: 15637964 INFO @ Fri, 26 Jun 2020 23:43:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:43:17: #1 finished! INFO @ Fri, 26 Jun 2020 23:43:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:43:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:43:19: #2 number of paired peaks: 353 WARNING @ Fri, 26 Jun 2020 23:43:19: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Fri, 26 Jun 2020 23:43:19: start model_add_line... INFO @ Fri, 26 Jun 2020 23:43:19: start X-correlation... INFO @ Fri, 26 Jun 2020 23:43:19: end of X-cor INFO @ Fri, 26 Jun 2020 23:43:19: #2 finished! INFO @ Fri, 26 Jun 2020 23:43:19: #2 predicted fragment length is 33 bps INFO @ Fri, 26 Jun 2020 23:43:19: #2 alternative fragment length(s) may be 3,33 bps INFO @ Fri, 26 Jun 2020 23:43:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.10_model.r WARNING @ Fri, 26 Jun 2020 23:43:19: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:43:19: #2 You may need to consider one of the other alternative d(s): 3,33 WARNING @ Fri, 26 Jun 2020 23:43:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:43:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:43:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:43:24: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:43:31: 12000000 INFO @ Fri, 26 Jun 2020 23:43:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:43:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:43:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.05_summits.bed INFO @ Fri, 26 Jun 2020 23:43:32: Done! pass1 - making usageList (586 chroms): 1 millis pass2 - checking and writing primary data (2468 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:43:39: 13000000 INFO @ Fri, 26 Jun 2020 23:43:46: 14000000 INFO @ Fri, 26 Jun 2020 23:43:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:43:53: 15000000 INFO @ Fri, 26 Jun 2020 23:43:58: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:43:58: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:43:58: #1 total tags in treatment: 15637964 INFO @ Fri, 26 Jun 2020 23:43:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:43:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:43:58: #1 tags after filtering in treatment: 15637964 INFO @ Fri, 26 Jun 2020 23:43:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:43:58: #1 finished! INFO @ Fri, 26 Jun 2020 23:43:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:43:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:43:59: #2 number of paired peaks: 353 WARNING @ Fri, 26 Jun 2020 23:43:59: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Fri, 26 Jun 2020 23:43:59: start model_add_line... INFO @ Fri, 26 Jun 2020 23:43:59: start X-correlation... INFO @ Fri, 26 Jun 2020 23:43:59: end of X-cor INFO @ Fri, 26 Jun 2020 23:43:59: #2 finished! INFO @ Fri, 26 Jun 2020 23:43:59: #2 predicted fragment length is 33 bps INFO @ Fri, 26 Jun 2020 23:43:59: #2 alternative fragment length(s) may be 3,33 bps INFO @ Fri, 26 Jun 2020 23:43:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.20_model.r WARNING @ Fri, 26 Jun 2020 23:43:59: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:43:59: #2 You may need to consider one of the other alternative d(s): 3,33 WARNING @ Fri, 26 Jun 2020 23:43:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:43:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:43:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:44:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:44:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:44:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.10_summits.bed INFO @ Fri, 26 Jun 2020 23:44:04: Done! pass1 - making usageList (465 chroms): 1 millis pass2 - checking and writing primary data (1476 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:44:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:44:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:44:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:44:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287909/SRX287909.20_summits.bed INFO @ Fri, 26 Jun 2020 23:44:46: Done! pass1 - making usageList (201 chroms): 1 millis pass2 - checking and writing primary data (435 records, 4 fields): 7 millis CompletedMACS2peakCalling