Job ID = 6368584 SRX = SRX5020810 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:18 prefetch.2.10.7: 1) Downloading 'SRR8201433'... 2020-06-16T00:24:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:53 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:53 prefetch.2.10.7: 1) 'SRR8201433' was downloaded successfully 2020-06-16T00:25:53 prefetch.2.10.7: 'SRR8201433' has 0 unresolved dependencies Read 19040438 spots for SRR8201433/SRR8201433.sra Written 19040438 spots for SRR8201433/SRR8201433.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: 00:06:21 19040438 reads; of these: 19040438 (100.00%) were unpaired; of these: 1291064 (6.78%) aligned 0 times 14860294 (78.05%) aligned exactly 1 time 2889080 (15.17%) aligned >1 times 93.22% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 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] 2118163 / 17749374 = 0.1193 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 09:38:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.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 09:38:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:31: 1000000 INFO @ Tue, 16 Jun 2020 09:38:38: 2000000 INFO @ Tue, 16 Jun 2020 09:38:46: 3000000 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 09:38:53: 4000000 INFO @ Tue, 16 Jun 2020 09:38:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.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 09:38:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:00: 5000000 INFO @ Tue, 16 Jun 2020 09:39:03: 1000000 INFO @ Tue, 16 Jun 2020 09:39:08: 6000000 INFO @ Tue, 16 Jun 2020 09:39:11: 2000000 INFO @ Tue, 16 Jun 2020 09:39:16: 7000000 INFO @ Tue, 16 Jun 2020 09:39:19: 3000000 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 09:39:24: 8000000 INFO @ Tue, 16 Jun 2020 09:39:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.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 09:39:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:27: 4000000 INFO @ Tue, 16 Jun 2020 09:39:32: 9000000 INFO @ Tue, 16 Jun 2020 09:39:33: 1000000 INFO @ Tue, 16 Jun 2020 09:39:36: 5000000 INFO @ Tue, 16 Jun 2020 09:39:40: 10000000 INFO @ Tue, 16 Jun 2020 09:39:41: 2000000 INFO @ Tue, 16 Jun 2020 09:39:44: 6000000 INFO @ Tue, 16 Jun 2020 09:39:48: 11000000 INFO @ Tue, 16 Jun 2020 09:39:49: 3000000 INFO @ Tue, 16 Jun 2020 09:39:53: 7000000 INFO @ Tue, 16 Jun 2020 09:39:56: 12000000 INFO @ Tue, 16 Jun 2020 09:39:57: 4000000 INFO @ Tue, 16 Jun 2020 09:40:02: 8000000 INFO @ Tue, 16 Jun 2020 09:40:04: 13000000 INFO @ Tue, 16 Jun 2020 09:40:05: 5000000 INFO @ Tue, 16 Jun 2020 09:40:10: 9000000 INFO @ Tue, 16 Jun 2020 09:40:12: 14000000 INFO @ Tue, 16 Jun 2020 09:40:13: 6000000 INFO @ Tue, 16 Jun 2020 09:40:19: 10000000 INFO @ Tue, 16 Jun 2020 09:40:20: 15000000 INFO @ Tue, 16 Jun 2020 09:40:22: 7000000 INFO @ Tue, 16 Jun 2020 09:40:25: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:40:25: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:40:25: #1 total tags in treatment: 15631211 INFO @ Tue, 16 Jun 2020 09:40:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:25: #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 09:40:25: #1 tags after filtering in treatment: 15631211 INFO @ Tue, 16 Jun 2020 09:40:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:26: #2 number of paired peaks: 231 WARNING @ Tue, 16 Jun 2020 09:40:26: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:26: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 09:40:26: #2 alternative fragment length(s) may be 3,70 bps INFO @ Tue, 16 Jun 2020 09:40:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.05_model.r WARNING @ Tue, 16 Jun 2020 09:40:26: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:26: #2 You may need to consider one of the other alternative d(s): 3,70 WARNING @ Tue, 16 Jun 2020 09:40:26: #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 09:40:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:27: 11000000 INFO @ Tue, 16 Jun 2020 09:40:30: 8000000 INFO @ Tue, 16 Jun 2020 09:40:36: 12000000 INFO @ Tue, 16 Jun 2020 09:40:38: 9000000 INFO @ Tue, 16 Jun 2020 09:40:44: 13000000 INFO @ Tue, 16 Jun 2020 09:40:46: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:40:53: 14000000 INFO @ Tue, 16 Jun 2020 09:40:54: 11000000 INFO @ Tue, 16 Jun 2020 09:40:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:01: 15000000 INFO @ Tue, 16 Jun 2020 09:41:02: 12000000 INFO @ Tue, 16 Jun 2020 09:41:07: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:41:07: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:41:07: #1 total tags in treatment: 15631211 INFO @ Tue, 16 Jun 2020 09:41:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:07: #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 09:41:07: #1 tags after filtering in treatment: 15631211 INFO @ Tue, 16 Jun 2020 09:41:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:08: #2 number of paired peaks: 231 WARNING @ Tue, 16 Jun 2020 09:41:08: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:08: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 09:41:08: #2 alternative fragment length(s) may be 3,70 bps INFO @ Tue, 16 Jun 2020 09:41:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.10_model.r WARNING @ Tue, 16 Jun 2020 09:41:08: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:08: #2 You may need to consider one of the other alternative d(s): 3,70 WARNING @ Tue, 16 Jun 2020 09:41:08: #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 09:41:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.05_summits.bed INFO @ Tue, 16 Jun 2020 09:41:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (581 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:10: 13000000 INFO @ Tue, 16 Jun 2020 09:41:18: 14000000 INFO @ Tue, 16 Jun 2020 09:41:25: 15000000 INFO @ Tue, 16 Jun 2020 09:41:30: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:41:30: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:41:30: #1 total tags in treatment: 15631211 INFO @ Tue, 16 Jun 2020 09:41:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:30: #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 09:41:30: #1 tags after filtering in treatment: 15631211 INFO @ Tue, 16 Jun 2020 09:41:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:31: #2 number of paired peaks: 231 WARNING @ Tue, 16 Jun 2020 09:41:31: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:32: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 09:41:32: #2 alternative fragment length(s) may be 3,70 bps INFO @ Tue, 16 Jun 2020 09:41:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.20_model.r WARNING @ Tue, 16 Jun 2020 09:41:32: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:32: #2 You may need to consider one of the other alternative d(s): 3,70 WARNING @ Tue, 16 Jun 2020 09:41:32: #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 09:41:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:41:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.10_summits.bed INFO @ Tue, 16 Jun 2020 09:41:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (417 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020810/SRX5020810.20_summits.bed INFO @ Tue, 16 Jun 2020 09:42:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 1 millis CompletedMACS2peakCalling