Job ID = 6368548 SRX = SRX5020775 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:20:22 prefetch.2.10.7: 1) Downloading 'SRR8201398'... 2020-06-16T00:20:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:13 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:13 prefetch.2.10.7: 1) 'SRR8201398' was downloaded successfully 2020-06-16T00:23:13 prefetch.2.10.7: 'SRR8201398' has 0 unresolved dependencies Read 19467594 spots for SRR8201398/SRR8201398.sra Written 19467594 spots for SRR8201398/SRR8201398.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: 00:06:44 19467594 reads; of these: 19467594 (100.00%) were unpaired; of these: 760203 (3.90%) aligned 0 times 15555542 (79.90%) aligned exactly 1 time 3151849 (16.19%) aligned >1 times 96.10% overall alignment rate Time searching: 00:06:44 Overall time: 00:06:44 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] 3061130 / 18707391 = 0.1636 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 09:36:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.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 09:36:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:43: 1000000 INFO @ Tue, 16 Jun 2020 09:36:49: 2000000 INFO @ Tue, 16 Jun 2020 09:36:55: 3000000 INFO @ Tue, 16 Jun 2020 09:37:01: 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 09:37:07: 5000000 INFO @ Tue, 16 Jun 2020 09:37:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.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 09:37:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:13: 6000000 INFO @ Tue, 16 Jun 2020 09:37:14: 1000000 INFO @ Tue, 16 Jun 2020 09:37:19: 7000000 INFO @ Tue, 16 Jun 2020 09:37:20: 2000000 INFO @ Tue, 16 Jun 2020 09:37:26: 8000000 INFO @ Tue, 16 Jun 2020 09:37:26: 3000000 INFO @ Tue, 16 Jun 2020 09:37:32: 9000000 INFO @ Tue, 16 Jun 2020 09:37:34: 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 09:37:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.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 09:37:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:39: 10000000 INFO @ Tue, 16 Jun 2020 09:37:41: 5000000 INFO @ Tue, 16 Jun 2020 09:37:45: 1000000 INFO @ Tue, 16 Jun 2020 09:37:46: 11000000 INFO @ Tue, 16 Jun 2020 09:37:48: 6000000 INFO @ Tue, 16 Jun 2020 09:37:52: 2000000 INFO @ Tue, 16 Jun 2020 09:37:53: 12000000 INFO @ Tue, 16 Jun 2020 09:37:55: 7000000 INFO @ Tue, 16 Jun 2020 09:37:59: 3000000 INFO @ Tue, 16 Jun 2020 09:38:00: 13000000 INFO @ Tue, 16 Jun 2020 09:38:02: 8000000 INFO @ Tue, 16 Jun 2020 09:38:06: 4000000 INFO @ Tue, 16 Jun 2020 09:38:07: 14000000 INFO @ Tue, 16 Jun 2020 09:38:09: 9000000 INFO @ Tue, 16 Jun 2020 09:38:13: 5000000 INFO @ Tue, 16 Jun 2020 09:38:14: 15000000 INFO @ Tue, 16 Jun 2020 09:38:16: 10000000 INFO @ Tue, 16 Jun 2020 09:38:19: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:38:19: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:38:19: #1 total tags in treatment: 15646261 INFO @ Tue, 16 Jun 2020 09:38:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:19: #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 09:38:19: #1 tags after filtering in treatment: 15646261 INFO @ Tue, 16 Jun 2020 09:38:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:20: 6000000 INFO @ Tue, 16 Jun 2020 09:38:20: #2 number of paired peaks: 313 WARNING @ Tue, 16 Jun 2020 09:38:20: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:20: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:38:20: #2 alternative fragment length(s) may be 4,78 bps INFO @ Tue, 16 Jun 2020 09:38:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.05_model.r WARNING @ Tue, 16 Jun 2020 09:38:20: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:38:20: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Tue, 16 Jun 2020 09:38:20: #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 09:38:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:23: 11000000 INFO @ Tue, 16 Jun 2020 09:38:27: 7000000 INFO @ Tue, 16 Jun 2020 09:38:30: 12000000 INFO @ Tue, 16 Jun 2020 09:38:33: 8000000 INFO @ Tue, 16 Jun 2020 09:38:36: 13000000 INFO @ Tue, 16 Jun 2020 09:38:40: 9000000 INFO @ Tue, 16 Jun 2020 09:38:43: 14000000 INFO @ Tue, 16 Jun 2020 09:38:47: 10000000 INFO @ Tue, 16 Jun 2020 09:38:50: 15000000 INFO @ Tue, 16 Jun 2020 09:38:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:54: 11000000 INFO @ Tue, 16 Jun 2020 09:38:54: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:38:54: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:38:54: #1 total tags in treatment: 15646261 INFO @ Tue, 16 Jun 2020 09:38:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:54: #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 09:38:55: #1 tags after filtering in treatment: 15646261 INFO @ Tue, 16 Jun 2020 09:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:56: #2 number of paired peaks: 313 WARNING @ Tue, 16 Jun 2020 09:38:56: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:56: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:38:56: #2 alternative fragment length(s) may be 4,78 bps INFO @ Tue, 16 Jun 2020 09:38:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.10_model.r WARNING @ Tue, 16 Jun 2020 09:38:56: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:38:56: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Tue, 16 Jun 2020 09:38:56: #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 09:38:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:56: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:39:00: 12000000 INFO @ Tue, 16 Jun 2020 09:39:07: 13000000 INFO @ Tue, 16 Jun 2020 09:39:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.05_summits.bed INFO @ Tue, 16 Jun 2020 09:39:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2660 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:39:13: 14000000 INFO @ Tue, 16 Jun 2020 09:39:20: 15000000 INFO @ Tue, 16 Jun 2020 09:39:24: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:39:24: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:39:24: #1 total tags in treatment: 15646261 INFO @ Tue, 16 Jun 2020 09:39:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:24: #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 09:39:24: #1 tags after filtering in treatment: 15646261 INFO @ Tue, 16 Jun 2020 09:39:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:25: #2 number of paired peaks: 313 WARNING @ Tue, 16 Jun 2020 09:39:25: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:25: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:39:25: #2 alternative fragment length(s) may be 4,78 bps INFO @ Tue, 16 Jun 2020 09:39:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.20_model.r WARNING @ Tue, 16 Jun 2020 09:39:25: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:39:25: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Tue, 16 Jun 2020 09:39:25: #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 09:39:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:39:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.10_summits.bed INFO @ Tue, 16 Jun 2020 09:39:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1454 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:39:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020775/SRX5020775.20_summits.bed INFO @ Tue, 16 Jun 2020 09:40:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (653 records, 4 fields): 1 millis CompletedMACS2peakCalling