Job ID = 6454486 SRX = SRX2165273 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:21:29 prefetch.2.10.7: 1) Downloading 'SRR4244775'... 2020-06-21T09:21:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:22:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:22:55 prefetch.2.10.7: 'SRR4244775' is valid 2020-06-21T09:22:55 prefetch.2.10.7: 1) 'SRR4244775' was downloaded successfully Read 8454590 spots for SRR4244775/SRR4244775.sra Written 8454590 spots for SRR4244775/SRR4244775.sra 2020-06-21T09:23:30 prefetch.2.10.7: 1) Downloading 'SRR4244776'... 2020-06-21T09:23:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:25:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:25:47 prefetch.2.10.7: 'SRR4244776' is valid 2020-06-21T09:25:47 prefetch.2.10.7: 1) 'SRR4244776' was downloaded successfully Read 9663745 spots for SRR4244776/SRR4244776.sra Written 9663745 spots for SRR4244776/SRR4244776.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: 00:05:19 18118335 reads; of these: 18118335 (100.00%) were unpaired; of these: 5075300 (28.01%) aligned 0 times 9549601 (52.71%) aligned exactly 1 time 3493434 (19.28%) aligned >1 times 71.99% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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] 4671326 / 13043035 = 0.3581 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 18:35:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.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 18:35:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:35:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:35:38: 1000000 INFO @ Sun, 21 Jun 2020 18:35:46: 2000000 INFO @ Sun, 21 Jun 2020 18:35:54: 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 18:36:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.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 18:36:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:36:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:36:02: 4000000 INFO @ Sun, 21 Jun 2020 18:36:09: 1000000 INFO @ Sun, 21 Jun 2020 18:36:10: 5000000 INFO @ Sun, 21 Jun 2020 18:36:17: 2000000 INFO @ Sun, 21 Jun 2020 18:36:19: 6000000 INFO @ Sun, 21 Jun 2020 18:36:25: 3000000 INFO @ Sun, 21 Jun 2020 18:36:28: 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 18:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.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 18:36:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:36:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:36:33: 4000000 INFO @ Sun, 21 Jun 2020 18:36:37: 8000000 INFO @ Sun, 21 Jun 2020 18:36:40: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:36:40: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:36:40: #1 total tags in treatment: 8371709 INFO @ Sun, 21 Jun 2020 18:36:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:40: #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 18:36:40: 1000000 INFO @ Sun, 21 Jun 2020 18:36:41: #1 tags after filtering in treatment: 8371706 INFO @ Sun, 21 Jun 2020 18:36:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:41: 5000000 INFO @ Sun, 21 Jun 2020 18:36:41: #2 number of paired peaks: 928 WARNING @ Sun, 21 Jun 2020 18:36:41: Fewer paired peaks (928) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 928 pairs to build model! INFO @ Sun, 21 Jun 2020 18:36:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:41: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 18:36:41: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sun, 21 Jun 2020 18:36:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.05_model.r WARNING @ Sun, 21 Jun 2020 18:36:41: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:36:41: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sun, 21 Jun 2020 18:36:41: #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 18:36:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:36:49: 6000000 INFO @ Sun, 21 Jun 2020 18:36:49: 2000000 INFO @ Sun, 21 Jun 2020 18:36:57: 7000000 INFO @ Sun, 21 Jun 2020 18:36:58: 3000000 INFO @ Sun, 21 Jun 2020 18:36:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:05: 8000000 INFO @ Sun, 21 Jun 2020 18:37:07: 4000000 INFO @ Sun, 21 Jun 2020 18:37:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.05_summits.bed INFO @ Sun, 21 Jun 2020 18:37:08: Done! INFO @ Sun, 21 Jun 2020 18:37:09: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:37:09: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:37:09: #1 total tags in treatment: 8371709 INFO @ Sun, 21 Jun 2020 18:37:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:37:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (662 chroms): 3 millis pass2 - checking and writing primary data (2500 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:37:09: #1 tags after filtering in treatment: 8371706 INFO @ Sun, 21 Jun 2020 18:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:37:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:37:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:37:10: #2 number of paired peaks: 928 WARNING @ Sun, 21 Jun 2020 18:37:10: Fewer paired peaks (928) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 928 pairs to build model! INFO @ Sun, 21 Jun 2020 18:37:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:37:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:37:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:37:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:37:10: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 18:37:10: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sun, 21 Jun 2020 18:37:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.10_model.r WARNING @ Sun, 21 Jun 2020 18:37:10: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:37:10: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sun, 21 Jun 2020 18:37:10: #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 18:37:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:37:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:37:15: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:37:23: 6000000 INFO @ Sun, 21 Jun 2020 18:37:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:32: 7000000 INFO @ Sun, 21 Jun 2020 18:37:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.10_summits.bed INFO @ Sun, 21 Jun 2020 18:37:37: Done! pass1 - making usageList (553 chroms): 1 millis pass2 - checking and writing primary data (1715 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:37:39: 8000000 INFO @ Sun, 21 Jun 2020 18:37:42: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:37:42: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:37:42: #1 total tags in treatment: 8371709 INFO @ Sun, 21 Jun 2020 18:37:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:37:42: #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 18:37:43: #1 tags after filtering in treatment: 8371706 INFO @ Sun, 21 Jun 2020 18:37:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:37:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:37:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:37:43: #2 number of paired peaks: 928 WARNING @ Sun, 21 Jun 2020 18:37:43: Fewer paired peaks (928) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 928 pairs to build model! INFO @ Sun, 21 Jun 2020 18:37:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:37:44: start X-correlation... INFO @ Sun, 21 Jun 2020 18:37:44: end of X-cor INFO @ Sun, 21 Jun 2020 18:37:44: #2 finished! INFO @ Sun, 21 Jun 2020 18:37:44: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 18:37:44: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sun, 21 Jun 2020 18:37:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.20_model.r WARNING @ Sun, 21 Jun 2020 18:37:44: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:37:44: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sun, 21 Jun 2020 18:37:44: #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 18:37:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:37:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:38:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:38:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:38:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165273/SRX2165273.20_summits.bed INFO @ Sun, 21 Jun 2020 18:38:10: Done! pass1 - making usageList (378 chroms): 1 millis pass2 - checking and writing primary data (784 records, 4 fields): 11 millis CompletedMACS2peakCalling