Job ID = 6366787 SRX = SRX233452 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:01:38 prefetch.2.10.7: 1) Downloading 'SRR701507'... 2020-06-15T23:01:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:54 prefetch.2.10.7: 'SRR701507' is valid 2020-06-15T23:01:54 prefetch.2.10.7: 1) 'SRR701507' was downloaded successfully Read 1012095 spots for SRR701507/SRR701507.sra Written 1012095 spots for SRR701507/SRR701507.sra 2020-06-15T23:02:13 prefetch.2.10.7: 1) Downloading 'SRR701508'... 2020-06-15T23:02:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:35 prefetch.2.10.7: 'SRR701508' is valid 2020-06-15T23:02:35 prefetch.2.10.7: 1) 'SRR701508' was downloaded successfully Read 3735786 spots for SRR701508/SRR701508.sra Written 3735786 spots for SRR701508/SRR701508.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: 00:00:27 4747881 reads; of these: 4747881 (100.00%) were unpaired; of these: 3450347 (72.67%) aligned 0 times 1055768 (22.24%) aligned exactly 1 time 241766 (5.09%) aligned >1 times 27.33% overall alignment rate Time searching: 00:00:27 Overall time: 00:00:27 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] 50544 / 1297534 = 0.0390 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 08:04:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.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 08:04:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:05: 1000000 INFO @ Tue, 16 Jun 2020 08:04:06: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:04:06: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:04:06: #1 total tags in treatment: 1246990 INFO @ Tue, 16 Jun 2020 08:04:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:06: #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 08:04:06: #1 tags after filtering in treatment: 1246990 INFO @ Tue, 16 Jun 2020 08:04:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:06: #2 number of paired peaks: 409 WARNING @ Tue, 16 Jun 2020 08:04:06: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:06: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:04:06: #2 alternative fragment length(s) may be 31,81,236,444,477,544,560 bps INFO @ Tue, 16 Jun 2020 08:04:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.05_model.r WARNING @ Tue, 16 Jun 2020 08:04:06: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:06: #2 You may need to consider one of the other alternative d(s): 31,81,236,444,477,544,560 WARNING @ Tue, 16 Jun 2020 08:04:06: #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 08:04:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.05_summits.bed INFO @ Tue, 16 Jun 2020 08:04:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (217 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:04:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.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 08:04:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:36: 1000000 INFO @ Tue, 16 Jun 2020 08:04:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:04:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:04:37: #1 total tags in treatment: 1246990 INFO @ Tue, 16 Jun 2020 08:04:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:37: #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 08:04:37: #1 tags after filtering in treatment: 1246990 INFO @ Tue, 16 Jun 2020 08:04:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:37: #2 number of paired peaks: 409 WARNING @ Tue, 16 Jun 2020 08:04:37: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:37: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:04:37: #2 alternative fragment length(s) may be 31,81,236,444,477,544,560 bps INFO @ Tue, 16 Jun 2020 08:04:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.10_model.r WARNING @ Tue, 16 Jun 2020 08:04:37: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:37: #2 You may need to consider one of the other alternative d(s): 31,81,236,444,477,544,560 WARNING @ Tue, 16 Jun 2020 08:04:37: #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 08:04:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.10_summits.bed INFO @ Tue, 16 Jun 2020 08:04:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (88 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:05:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.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 08:05:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:00: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:05:06: 1000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:05:07: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:05:07: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:05:07: #1 total tags in treatment: 1246990 INFO @ Tue, 16 Jun 2020 08:05:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:07: #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 08:05:07: #1 tags after filtering in treatment: 1246990 INFO @ Tue, 16 Jun 2020 08:05:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:07: #2 number of paired peaks: 409 WARNING @ Tue, 16 Jun 2020 08:05:07: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:07: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:05:07: #2 alternative fragment length(s) may be 31,81,236,444,477,544,560 bps INFO @ Tue, 16 Jun 2020 08:05:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.20_model.r WARNING @ Tue, 16 Jun 2020 08:05:07: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:07: #2 You may need to consider one of the other alternative d(s): 31,81,236,444,477,544,560 WARNING @ Tue, 16 Jun 2020 08:05:07: #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 08:05:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233452/SRX233452.20_summits.bed INFO @ Tue, 16 Jun 2020 08:05:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (31 records, 4 fields): 1 millis CompletedMACS2peakCalling