Job ID = 6366986 SRX = SRX257685 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:16:16 prefetch.2.10.7: 1) Downloading 'SRR800701'... 2020-06-15T23:16:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:17:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:17:35 prefetch.2.10.7: 'SRR800701' is valid 2020-06-15T23:17:35 prefetch.2.10.7: 1) 'SRR800701' was downloaded successfully Read 11492792 spots for SRR800701/SRR800701.sra Written 11492792 spots for SRR800701/SRR800701.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: 00:02:54 11492792 reads; of these: 11492792 (100.00%) were unpaired; of these: 372345 (3.24%) aligned 0 times 9213279 (80.17%) aligned exactly 1 time 1907168 (16.59%) aligned >1 times 96.76% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 847141 / 11120447 = 0.0762 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 @ Tue, 16 Jun 2020 08:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:24:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:45: 1000000 INFO @ Tue, 16 Jun 2020 08:24:51: 2000000 INFO @ Tue, 16 Jun 2020 08:24:57: 3000000 INFO @ Tue, 16 Jun 2020 08:25:03: 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 @ Tue, 16 Jun 2020 08:25:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:25:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:10: 5000000 INFO @ Tue, 16 Jun 2020 08:25:15: 1000000 INFO @ Tue, 16 Jun 2020 08:25:17: 6000000 INFO @ Tue, 16 Jun 2020 08:25:22: 2000000 INFO @ Tue, 16 Jun 2020 08:25:23: 7000000 INFO @ Tue, 16 Jun 2020 08:25:29: 3000000 INFO @ Tue, 16 Jun 2020 08:25:30: 8000000 INFO @ Tue, 16 Jun 2020 08:25:36: 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 @ Tue, 16 Jun 2020 08:25:37: 9000000 INFO @ Tue, 16 Jun 2020 08:25:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:25:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:43: 5000000 INFO @ Tue, 16 Jun 2020 08:25:44: 10000000 INFO @ Tue, 16 Jun 2020 08:25:46: 1000000 INFO @ Tue, 16 Jun 2020 08:25:46: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:46: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:46: #1 total tags in treatment: 10273306 INFO @ Tue, 16 Jun 2020 08:25:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:25:46: #1 tags after filtering in treatment: 10273306 INFO @ Tue, 16 Jun 2020 08:25:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:47: #2 number of paired peaks: 337 WARNING @ Tue, 16 Jun 2020 08:25:47: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:47: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:25:47: #2 alternative fragment length(s) may be 3,50,557,565 bps INFO @ Tue, 16 Jun 2020 08:25:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.05_model.r WARNING @ Tue, 16 Jun 2020 08:25:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:25:47: #2 You may need to consider one of the other alternative d(s): 3,50,557,565 WARNING @ Tue, 16 Jun 2020 08:25:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:25:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:50: 6000000 INFO @ Tue, 16 Jun 2020 08:25:52: 2000000 INFO @ Tue, 16 Jun 2020 08:25:57: 7000000 INFO @ Tue, 16 Jun 2020 08:25:59: 3000000 INFO @ Tue, 16 Jun 2020 08:26:04: 8000000 INFO @ Tue, 16 Jun 2020 08:26:06: 4000000 INFO @ Tue, 16 Jun 2020 08:26:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:10: 9000000 INFO @ Tue, 16 Jun 2020 08:26:13: 5000000 INFO @ Tue, 16 Jun 2020 08:26:17: 10000000 INFO @ Tue, 16 Jun 2020 08:26:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.05_summits.bed INFO @ Tue, 16 Jun 2020 08:26:19: Done! INFO @ Tue, 16 Jun 2020 08:26:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:19: #1 total tags in treatment: 10273306 INFO @ Tue, 16 Jun 2020 08:26:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (640 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:19: #1 tags after filtering in treatment: 10273306 INFO @ Tue, 16 Jun 2020 08:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:20: 6000000 INFO @ Tue, 16 Jun 2020 08:26:20: #2 number of paired peaks: 337 WARNING @ Tue, 16 Jun 2020 08:26:20: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:20: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:26:20: #2 alternative fragment length(s) may be 3,50,557,565 bps INFO @ Tue, 16 Jun 2020 08:26:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.10_model.r WARNING @ Tue, 16 Jun 2020 08:26:20: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:20: #2 You may need to consider one of the other alternative d(s): 3,50,557,565 WARNING @ Tue, 16 Jun 2020 08:26:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:26:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:26: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:32: 8000000 INFO @ Tue, 16 Jun 2020 08:26:38: 9000000 INFO @ Tue, 16 Jun 2020 08:26:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:44: 10000000 INFO @ Tue, 16 Jun 2020 08:26:46: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:46: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:46: #1 total tags in treatment: 10273306 INFO @ Tue, 16 Jun 2020 08:26:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:26:46: #1 tags after filtering in treatment: 10273306 INFO @ Tue, 16 Jun 2020 08:26:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:47: #2 number of paired peaks: 337 WARNING @ Tue, 16 Jun 2020 08:26:47: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:47: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:26:47: #2 alternative fragment length(s) may be 3,50,557,565 bps INFO @ Tue, 16 Jun 2020 08:26:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.20_model.r WARNING @ Tue, 16 Jun 2020 08:26:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:47: #2 You may need to consider one of the other alternative d(s): 3,50,557,565 WARNING @ Tue, 16 Jun 2020 08:26:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:26:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.10_summits.bed INFO @ Tue, 16 Jun 2020 08:26:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:27:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257685/SRX257685.20_summits.bed INFO @ Tue, 16 Jun 2020 08:27:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 1 millis CompletedMACS2peakCalling