Job ID = 6459292 SRX = SRX661229 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:07:46 prefetch.2.10.7: 1) Downloading 'SRR1524957'... 2020-06-21T13:07:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:09:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:09:30 prefetch.2.10.7: 'SRR1524957' is valid 2020-06-21T13:09:30 prefetch.2.10.7: 1) 'SRR1524957' was downloaded successfully Read 15006773 spots for SRR1524957/SRR1524957.sra Written 15006773 spots for SRR1524957/SRR1524957.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: 00:03:24 15006773 reads; of these: 15006773 (100.00%) were unpaired; of these: 690866 (4.60%) aligned 0 times 12580127 (83.83%) aligned exactly 1 time 1735780 (11.57%) aligned >1 times 95.40% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 2069711 / 14315907 = 0.1446 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 22:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.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 22:18:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:44: 1000000 INFO @ Sun, 21 Jun 2020 22:18:51: 2000000 INFO @ Sun, 21 Jun 2020 22:18:57: 3000000 INFO @ Sun, 21 Jun 2020 22:19:04: 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 22:19:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.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 22:19:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:19:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:19:11: 5000000 INFO @ Sun, 21 Jun 2020 22:19:14: 1000000 INFO @ Sun, 21 Jun 2020 22:19:17: 6000000 INFO @ Sun, 21 Jun 2020 22:19:20: 2000000 INFO @ Sun, 21 Jun 2020 22:19:24: 7000000 INFO @ Sun, 21 Jun 2020 22:19:26: 3000000 INFO @ Sun, 21 Jun 2020 22:19:30: 8000000 INFO @ Sun, 21 Jun 2020 22:19:32: 4000000 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 22:19:37: 9000000 INFO @ Sun, 21 Jun 2020 22:19:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.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 22:19:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:19:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:19:39: 5000000 INFO @ Sun, 21 Jun 2020 22:19:44: 1000000 INFO @ Sun, 21 Jun 2020 22:19:44: 10000000 INFO @ Sun, 21 Jun 2020 22:19:45: 6000000 INFO @ Sun, 21 Jun 2020 22:19:50: 2000000 INFO @ Sun, 21 Jun 2020 22:19:51: 11000000 INFO @ Sun, 21 Jun 2020 22:19:52: 7000000 INFO @ Sun, 21 Jun 2020 22:19:57: 3000000 INFO @ Sun, 21 Jun 2020 22:19:57: 12000000 INFO @ Sun, 21 Jun 2020 22:19:58: 8000000 INFO @ Sun, 21 Jun 2020 22:19:59: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 22:19:59: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 22:19:59: #1 total tags in treatment: 12246196 INFO @ Sun, 21 Jun 2020 22:19:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:59: #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 22:20:00: #1 tags after filtering in treatment: 12246069 INFO @ Sun, 21 Jun 2020 22:20:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:20:00: #1 finished! INFO @ Sun, 21 Jun 2020 22:20:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:20:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:20:01: #2 number of paired peaks: 177 WARNING @ Sun, 21 Jun 2020 22:20:01: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sun, 21 Jun 2020 22:20:01: start model_add_line... INFO @ Sun, 21 Jun 2020 22:20:01: start X-correlation... INFO @ Sun, 21 Jun 2020 22:20:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:20:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:20:01: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 22:20:01: #2 alternative fragment length(s) may be 1,50,130,568,589 bps INFO @ Sun, 21 Jun 2020 22:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.05_model.r WARNING @ Sun, 21 Jun 2020 22:20:01: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:20:01: #2 You may need to consider one of the other alternative d(s): 1,50,130,568,589 WARNING @ Sun, 21 Jun 2020 22:20:01: #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 22:20:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:20:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:20:04: 4000000 INFO @ Sun, 21 Jun 2020 22:20:05: 9000000 INFO @ Sun, 21 Jun 2020 22:20:10: 5000000 INFO @ Sun, 21 Jun 2020 22:20:12: 10000000 INFO @ Sun, 21 Jun 2020 22:20:17: 6000000 INFO @ Sun, 21 Jun 2020 22:20:18: 11000000 INFO @ Sun, 21 Jun 2020 22:20:23: 7000000 INFO @ Sun, 21 Jun 2020 22:20:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:20:25: 12000000 INFO @ Sun, 21 Jun 2020 22:20:27: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 22:20:27: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 22:20:27: #1 total tags in treatment: 12246196 INFO @ Sun, 21 Jun 2020 22:20:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:20:27: #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 22:20:27: #1 tags after filtering in treatment: 12246069 INFO @ Sun, 21 Jun 2020 22:20:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:20:27: #1 finished! INFO @ Sun, 21 Jun 2020 22:20:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:20:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:20:28: #2 number of paired peaks: 177 WARNING @ Sun, 21 Jun 2020 22:20:28: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sun, 21 Jun 2020 22:20:28: start model_add_line... INFO @ Sun, 21 Jun 2020 22:20:28: start X-correlation... INFO @ Sun, 21 Jun 2020 22:20:28: end of X-cor INFO @ Sun, 21 Jun 2020 22:20:28: #2 finished! INFO @ Sun, 21 Jun 2020 22:20:28: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 22:20:28: #2 alternative fragment length(s) may be 1,50,130,568,589 bps INFO @ Sun, 21 Jun 2020 22:20:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.10_model.r WARNING @ Sun, 21 Jun 2020 22:20:28: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:20:28: #2 You may need to consider one of the other alternative d(s): 1,50,130,568,589 WARNING @ Sun, 21 Jun 2020 22:20:28: #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 22:20:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:20:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:20:29: 8000000 INFO @ Sun, 21 Jun 2020 22:20:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:20:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:20:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.05_summits.bed INFO @ Sun, 21 Jun 2020 22:20:35: Done! INFO @ Sun, 21 Jun 2020 22:20:35: 9000000 pass1 - making usageList (153 chroms): 1 millis pass2 - checking and writing primary data (412 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:20:42: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:20:48: 11000000 INFO @ Sun, 21 Jun 2020 22:20:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:20:54: 12000000 INFO @ Sun, 21 Jun 2020 22:20:56: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 22:20:56: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 22:20:56: #1 total tags in treatment: 12246196 INFO @ Sun, 21 Jun 2020 22:20:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:20:56: #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 22:20:56: #1 tags after filtering in treatment: 12246069 INFO @ Sun, 21 Jun 2020 22:20:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:20:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:20:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:20:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:20:57: #2 number of paired peaks: 177 WARNING @ Sun, 21 Jun 2020 22:20:57: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sun, 21 Jun 2020 22:20:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:20:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:20:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:20:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:20:57: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 22:20:57: #2 alternative fragment length(s) may be 1,50,130,568,589 bps INFO @ Sun, 21 Jun 2020 22:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.20_model.r WARNING @ Sun, 21 Jun 2020 22:20:57: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:20:57: #2 You may need to consider one of the other alternative d(s): 1,50,130,568,589 WARNING @ Sun, 21 Jun 2020 22:20:57: #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 22:20:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:20:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:21:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:21:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:21:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.10_summits.bed INFO @ Sun, 21 Jun 2020 22:21:02: Done! pass1 - making usageList (91 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:21:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:21:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:21:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:21:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX661229/SRX661229.20_summits.bed INFO @ Sun, 21 Jun 2020 22:21:31: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 4 millis CompletedMACS2peakCalling