Job ID = 6454827 SRX = SRX2592423 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:37:55 prefetch.2.10.7: 1) Downloading 'SRR5289700'... 2020-06-21T09:37:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:41:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:41:47 prefetch.2.10.7: 1) 'SRR5289700' was downloaded successfully Read 22538420 spots for SRR5289700/SRR5289700.sra Written 22538420 spots for SRR5289700/SRR5289700.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: 00:08:31 22538420 reads; of these: 22538420 (100.00%) were unpaired; of these: 1747891 (7.76%) aligned 0 times 15475886 (68.66%) aligned exactly 1 time 5314643 (23.58%) aligned >1 times 92.24% overall alignment rate Time searching: 00:08:31 Overall time: 00:08:31 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 12 files... [bam_rmdupse_core] 4724093 / 20790529 = 0.2272 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 18:58:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.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 18:58:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:52: 1000000 INFO @ Sun, 21 Jun 2020 18:58:58: 2000000 INFO @ Sun, 21 Jun 2020 18:59:04: 3000000 INFO @ Sun, 21 Jun 2020 18:59:10: 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 18:59:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.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 18:59:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:17: 5000000 INFO @ Sun, 21 Jun 2020 18:59:23: 1000000 INFO @ Sun, 21 Jun 2020 18:59:24: 6000000 INFO @ Sun, 21 Jun 2020 18:59:30: 2000000 INFO @ Sun, 21 Jun 2020 18:59:31: 7000000 INFO @ Sun, 21 Jun 2020 18:59:37: 3000000 INFO @ Sun, 21 Jun 2020 18:59:38: 8000000 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 18:59:44: 4000000 INFO @ Sun, 21 Jun 2020 18:59:45: 9000000 INFO @ Sun, 21 Jun 2020 18:59:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.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 18:59:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:51: 5000000 INFO @ Sun, 21 Jun 2020 18:59:52: 10000000 INFO @ Sun, 21 Jun 2020 18:59:54: 1000000 INFO @ Sun, 21 Jun 2020 18:59:57: 6000000 INFO @ Sun, 21 Jun 2020 18:59:59: 11000000 INFO @ Sun, 21 Jun 2020 19:00:02: 2000000 INFO @ Sun, 21 Jun 2020 19:00:04: 7000000 INFO @ Sun, 21 Jun 2020 19:00:06: 12000000 INFO @ Sun, 21 Jun 2020 19:00:09: 3000000 INFO @ Sun, 21 Jun 2020 19:00:11: 8000000 INFO @ Sun, 21 Jun 2020 19:00:13: 13000000 INFO @ Sun, 21 Jun 2020 19:00:17: 4000000 INFO @ Sun, 21 Jun 2020 19:00:18: 9000000 INFO @ Sun, 21 Jun 2020 19:00:20: 14000000 INFO @ Sun, 21 Jun 2020 19:00:25: 10000000 INFO @ Sun, 21 Jun 2020 19:00:25: 5000000 INFO @ Sun, 21 Jun 2020 19:00:28: 15000000 INFO @ Sun, 21 Jun 2020 19:00:32: 11000000 INFO @ Sun, 21 Jun 2020 19:00:33: 6000000 INFO @ Sun, 21 Jun 2020 19:00:35: 16000000 INFO @ Sun, 21 Jun 2020 19:00:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:00:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:00:36: #1 total tags in treatment: 16066436 INFO @ Sun, 21 Jun 2020 19:00:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:36: #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 19:00:36: #1 tags after filtering in treatment: 16066354 INFO @ Sun, 21 Jun 2020 19:00:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:38: #2 number of paired peaks: 216 WARNING @ Sun, 21 Jun 2020 19:00:38: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sun, 21 Jun 2020 19:00:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:38: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:00:38: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sun, 21 Jun 2020 19:00:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.05_model.r WARNING @ Sun, 21 Jun 2020 19:00:38: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:00:38: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sun, 21 Jun 2020 19:00:38: #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 19:00:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:39: 12000000 INFO @ Sun, 21 Jun 2020 19:00:39: 7000000 INFO @ Sun, 21 Jun 2020 19:00:46: 8000000 INFO @ Sun, 21 Jun 2020 19:00:46: 13000000 INFO @ Sun, 21 Jun 2020 19:00:53: 9000000 INFO @ Sun, 21 Jun 2020 19:00:53: 14000000 INFO @ Sun, 21 Jun 2020 19:00:59: 10000000 INFO @ Sun, 21 Jun 2020 19:00:59: 15000000 INFO @ Sun, 21 Jun 2020 19:01:06: 11000000 INFO @ Sun, 21 Jun 2020 19:01:06: 16000000 INFO @ Sun, 21 Jun 2020 19:01:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:01:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:01:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:01:07: #1 total tags in treatment: 16066436 INFO @ Sun, 21 Jun 2020 19:01:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:07: #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 19:01:08: #1 tags after filtering in treatment: 16066354 INFO @ Sun, 21 Jun 2020 19:01:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:01:09: #2 number of paired peaks: 216 WARNING @ Sun, 21 Jun 2020 19:01:09: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sun, 21 Jun 2020 19:01:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:09: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:01:09: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sun, 21 Jun 2020 19:01:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.10_model.r WARNING @ Sun, 21 Jun 2020 19:01:09: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:01:09: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sun, 21 Jun 2020 19:01:09: #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 19:01:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:12: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:01:19: 13000000 INFO @ Sun, 21 Jun 2020 19:01:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.05_summits.bed INFO @ Sun, 21 Jun 2020 19:01:22: Done! pass1 - making usageList (693 chroms): 3 millis pass2 - checking and writing primary data (12980 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:01:25: 14000000 INFO @ Sun, 21 Jun 2020 19:01:31: 15000000 INFO @ Sun, 21 Jun 2020 19:01:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:01:38: 16000000 INFO @ Sun, 21 Jun 2020 19:01:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:01:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:01:38: #1 total tags in treatment: 16066436 INFO @ Sun, 21 Jun 2020 19:01:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:38: #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 19:01:39: #1 tags after filtering in treatment: 16066354 INFO @ Sun, 21 Jun 2020 19:01:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:01:40: #2 number of paired peaks: 216 WARNING @ Sun, 21 Jun 2020 19:01:40: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sun, 21 Jun 2020 19:01:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:40: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:01:40: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sun, 21 Jun 2020 19:01:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.20_model.r WARNING @ Sun, 21 Jun 2020 19:01:40: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:01:40: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sun, 21 Jun 2020 19:01:40: #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 19:01:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.10_summits.bed INFO @ Sun, 21 Jun 2020 19:01:51: Done! pass1 - making usageList (482 chroms): 2 millis pass2 - checking and writing primary data (7239 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:02:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592423/SRX2592423.20_summits.bed INFO @ Sun, 21 Jun 2020 19:02:22: Done! pass1 - making usageList (191 chroms): 1 millis pass2 - checking and writing primary data (930 records, 4 fields): 12 millis CompletedMACS2peakCalling