Job ID = 6368662 SRX = SRX529222 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:16 prefetch.2.10.7: 1) Downloading 'SRR1265826'... 2020-06-16T00:26:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:02 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:02 prefetch.2.10.7: 'SRR1265826' is valid 2020-06-16T00:27:02 prefetch.2.10.7: 1) 'SRR1265826' was downloaded successfully Read 5595479 spots for SRR1265826/SRR1265826.sra Written 5595479 spots for SRR1265826/SRR1265826.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: 00:01:21 5595479 reads; of these: 5595479 (100.00%) were unpaired; of these: 127554 (2.28%) aligned 0 times 4499845 (80.42%) aligned exactly 1 time 968080 (17.30%) aligned >1 times 97.72% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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_rmdupse_core] 319709 / 5467925 = 0.0585 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 09:30:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.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 09:30:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:34: 1000000 INFO @ Tue, 16 Jun 2020 09:30:40: 2000000 INFO @ Tue, 16 Jun 2020 09:30:45: 3000000 INFO @ Tue, 16 Jun 2020 09:30:51: 4000000 INFO @ Tue, 16 Jun 2020 09:30:56: 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 09:30:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:30:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:30:57: #1 total tags in treatment: 5148216 INFO @ Tue, 16 Jun 2020 09:30:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:57: #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 09:30:57: #1 tags after filtering in treatment: 5148216 INFO @ Tue, 16 Jun 2020 09:30:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:57: #2 number of paired peaks: 441 WARNING @ Tue, 16 Jun 2020 09:30:57: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:58: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:30:58: #2 alternative fragment length(s) may be 4,48,483,502 bps INFO @ Tue, 16 Jun 2020 09:30:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.05_model.r WARNING @ Tue, 16 Jun 2020 09:30:58: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:58: #2 You may need to consider one of the other alternative d(s): 4,48,483,502 WARNING @ Tue, 16 Jun 2020 09:30:58: #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 09:30:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.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 09:30:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:05: 1000000 INFO @ Tue, 16 Jun 2020 09:31:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:11: 2000000 INFO @ Tue, 16 Jun 2020 09:31:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.05_summits.bed INFO @ Tue, 16 Jun 2020 09:31:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (565 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:17: 3000000 INFO @ Tue, 16 Jun 2020 09:31:24: 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 09:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.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 09:31:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:30: 5000000 INFO @ Tue, 16 Jun 2020 09:31:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:31:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:31:31: #1 total tags in treatment: 5148216 INFO @ Tue, 16 Jun 2020 09:31:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:31: #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 09:31:31: #1 tags after filtering in treatment: 5148216 INFO @ Tue, 16 Jun 2020 09:31:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:31: #2 number of paired peaks: 441 WARNING @ Tue, 16 Jun 2020 09:31:31: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:31: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:31:31: #2 alternative fragment length(s) may be 4,48,483,502 bps INFO @ Tue, 16 Jun 2020 09:31:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.10_model.r WARNING @ Tue, 16 Jun 2020 09:31:31: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:31: #2 You may need to consider one of the other alternative d(s): 4,48,483,502 WARNING @ Tue, 16 Jun 2020 09:31:31: #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 09:31:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:35: 1000000 INFO @ Tue, 16 Jun 2020 09:31:40: 2000000 INFO @ Tue, 16 Jun 2020 09:31:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:46: 3000000 INFO @ Tue, 16 Jun 2020 09:31:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.10_summits.bed INFO @ Tue, 16 Jun 2020 09:31:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (343 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:51: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:31:56: 5000000 INFO @ Tue, 16 Jun 2020 09:31:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:31:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:31:57: #1 total tags in treatment: 5148216 INFO @ Tue, 16 Jun 2020 09:31:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:57: #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 09:31:57: #1 tags after filtering in treatment: 5148216 INFO @ Tue, 16 Jun 2020 09:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:58: #2 number of paired peaks: 441 WARNING @ Tue, 16 Jun 2020 09:31:58: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:58: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:31:58: #2 alternative fragment length(s) may be 4,48,483,502 bps INFO @ Tue, 16 Jun 2020 09:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.20_model.r WARNING @ Tue, 16 Jun 2020 09:31:58: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:58: #2 You may need to consider one of the other alternative d(s): 4,48,483,502 WARNING @ Tue, 16 Jun 2020 09:31:58: #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 09:31:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:32:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529222/SRX529222.20_summits.bed INFO @ Tue, 16 Jun 2020 09:32:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (142 records, 4 fields): 1 millis CompletedMACS2peakCalling