Job ID = 6366458 SRX = SRX147611 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:59:08 prefetch.2.10.7: 1) Downloading 'SRR496288'... 2020-06-15T22:59:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:33 prefetch.2.10.7: 'SRR496288' is valid 2020-06-15T22:59:33 prefetch.2.10.7: 1) 'SRR496288' was downloaded successfully Read 6937918 spots for SRR496288/SRR496288.sra Written 6937918 spots for SRR496288/SRR496288.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: 00:01:14 6937918 reads; of these: 6937918 (100.00%) were unpaired; of these: 169310 (2.44%) aligned 0 times 5541052 (79.87%) aligned exactly 1 time 1227556 (17.69%) aligned >1 times 97.56% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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_rmdupse_core] 568551 / 6768608 = 0.0840 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 08:02:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.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 08:02:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:59: 1000000 INFO @ Tue, 16 Jun 2020 08:03:04: 2000000 INFO @ Tue, 16 Jun 2020 08:03:09: 3000000 INFO @ Tue, 16 Jun 2020 08:03:14: 4000000 INFO @ Tue, 16 Jun 2020 08:03:19: 5000000 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 08:03:24: 6000000 INFO @ Tue, 16 Jun 2020 08:03:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.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 08:03:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:25: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:03:25: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:03:25: #1 total tags in treatment: 6200057 INFO @ Tue, 16 Jun 2020 08:03:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:25: #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 08:03:25: #1 tags after filtering in treatment: 6200057 INFO @ Tue, 16 Jun 2020 08:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:26: #2 number of paired peaks: 423 WARNING @ Tue, 16 Jun 2020 08:03:26: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:26: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 08:03:26: #2 alternative fragment length(s) may be 2,28,516,588 bps INFO @ Tue, 16 Jun 2020 08:03:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.05_model.r WARNING @ Tue, 16 Jun 2020 08:03:26: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:03:26: #2 You may need to consider one of the other alternative d(s): 2,28,516,588 WARNING @ Tue, 16 Jun 2020 08:03:26: #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 08:03:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:30: 1000000 INFO @ Tue, 16 Jun 2020 08:03:35: 2000000 INFO @ Tue, 16 Jun 2020 08:03:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:40: 3000000 INFO @ Tue, 16 Jun 2020 08:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.05_summits.bed INFO @ Tue, 16 Jun 2020 08:03:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (597 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:03:45: 4000000 INFO @ Tue, 16 Jun 2020 08:03:50: 5000000 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 08:03:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.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 08:03:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:55: 6000000 INFO @ Tue, 16 Jun 2020 08:03:56: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:03:56: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:03:56: #1 total tags in treatment: 6200057 INFO @ Tue, 16 Jun 2020 08:03:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:56: #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 08:03:56: #1 tags after filtering in treatment: 6200057 INFO @ Tue, 16 Jun 2020 08:03:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:57: #2 number of paired peaks: 423 WARNING @ Tue, 16 Jun 2020 08:03:57: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:57: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 08:03:57: #2 alternative fragment length(s) may be 2,28,516,588 bps INFO @ Tue, 16 Jun 2020 08:03:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.10_model.r WARNING @ Tue, 16 Jun 2020 08:03:57: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:03:57: #2 You may need to consider one of the other alternative d(s): 2,28,516,588 WARNING @ Tue, 16 Jun 2020 08:03:57: #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 08:03:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:00: 1000000 INFO @ Tue, 16 Jun 2020 08:04:05: 2000000 INFO @ Tue, 16 Jun 2020 08:04:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:10: 3000000 INFO @ Tue, 16 Jun 2020 08:04:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.10_summits.bed INFO @ Tue, 16 Jun 2020 08:04:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (270 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:16: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:04:21: 5000000 INFO @ Tue, 16 Jun 2020 08:04:26: 6000000 INFO @ Tue, 16 Jun 2020 08:04:27: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:04:27: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:04:27: #1 total tags in treatment: 6200057 INFO @ Tue, 16 Jun 2020 08:04:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:27: #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 08:04:27: #1 tags after filtering in treatment: 6200057 INFO @ Tue, 16 Jun 2020 08:04:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:28: #2 number of paired peaks: 423 WARNING @ Tue, 16 Jun 2020 08:04:28: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:28: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 08:04:28: #2 alternative fragment length(s) may be 2,28,516,588 bps INFO @ Tue, 16 Jun 2020 08:04:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.20_model.r WARNING @ Tue, 16 Jun 2020 08:04:28: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:28: #2 You may need to consider one of the other alternative d(s): 2,28,516,588 WARNING @ Tue, 16 Jun 2020 08:04:28: #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 08:04:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:04:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX147611/SRX147611.20_summits.bed INFO @ Tue, 16 Jun 2020 08:04:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (57 records, 4 fields): 1 millis CompletedMACS2peakCalling