Job ID = 6366802 SRX = SRX234910 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:39 prefetch.2.10.7: 1) Downloading 'SRR707554'... 2020-06-15T23:05:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:04 prefetch.2.10.7: 'SRR707554' is valid 2020-06-15T23:06:04 prefetch.2.10.7: 1) 'SRR707554' was downloaded successfully Read 4405220 spots for SRR707554/SRR707554.sra Written 4405220 spots for SRR707554/SRR707554.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: 00:00:40 4405220 reads; of these: 4405220 (100.00%) were unpaired; of these: 538456 (12.22%) aligned 0 times 3147364 (71.45%) aligned exactly 1 time 719400 (16.33%) aligned >1 times 87.78% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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] 267446 / 3866764 = 0.0692 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 08:08:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.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 08:08:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:21: 1000000 INFO @ Tue, 16 Jun 2020 08:08:26: 2000000 INFO @ Tue, 16 Jun 2020 08:08:31: 3000000 INFO @ Tue, 16 Jun 2020 08:08:34: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:08:34: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:08:34: #1 total tags in treatment: 3599318 INFO @ Tue, 16 Jun 2020 08:08:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:34: #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 08:08:34: #1 tags after filtering in treatment: 3599318 INFO @ Tue, 16 Jun 2020 08:08:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:34: #2 number of paired peaks: 521 WARNING @ Tue, 16 Jun 2020 08:08:34: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:34: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:08:34: #2 alternative fragment length(s) may be 3,34,492,499,511,553 bps INFO @ Tue, 16 Jun 2020 08:08:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.05_model.r WARNING @ Tue, 16 Jun 2020 08:08:34: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:34: #2 You may need to consider one of the other alternative d(s): 3,34,492,499,511,553 WARNING @ Tue, 16 Jun 2020 08:08:34: #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 08:08:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:43: #3 Call peaks for each chromosome... 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 08:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.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 08:08:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (462 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:51: 1000000 INFO @ Tue, 16 Jun 2020 08:08:56: 2000000 INFO @ Tue, 16 Jun 2020 08:09:02: 3000000 INFO @ Tue, 16 Jun 2020 08:09:05: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:09:05: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:09:05: #1 total tags in treatment: 3599318 INFO @ Tue, 16 Jun 2020 08:09:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:05: #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 08:09:05: #1 tags after filtering in treatment: 3599318 INFO @ Tue, 16 Jun 2020 08:09:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:05: #2 number of paired peaks: 521 WARNING @ Tue, 16 Jun 2020 08:09:05: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:05: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:09:05: #2 alternative fragment length(s) may be 3,34,492,499,511,553 bps INFO @ Tue, 16 Jun 2020 08:09:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.10_model.r WARNING @ Tue, 16 Jun 2020 08:09:05: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:09:05: #2 You may need to consider one of the other alternative d(s): 3,34,492,499,511,553 WARNING @ Tue, 16 Jun 2020 08:09:05: #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 08:09:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:13: #3 Call peaks for each chromosome... 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 08:09:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.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 08:09:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.10_summits.bed INFO @ Tue, 16 Jun 2020 08:09:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (235 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:09:22: 1000000 INFO @ Tue, 16 Jun 2020 08:09:28: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:09:33: 3000000 INFO @ Tue, 16 Jun 2020 08:09:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:09:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:09:37: #1 total tags in treatment: 3599318 INFO @ Tue, 16 Jun 2020 08:09:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:37: #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 08:09:37: #1 tags after filtering in treatment: 3599318 INFO @ Tue, 16 Jun 2020 08:09:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:37: #2 number of paired peaks: 521 WARNING @ Tue, 16 Jun 2020 08:09:37: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:37: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:09:37: #2 alternative fragment length(s) may be 3,34,492,499,511,553 bps INFO @ Tue, 16 Jun 2020 08:09:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.20_model.r WARNING @ Tue, 16 Jun 2020 08:09:37: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:09:37: #2 You may need to consider one of the other alternative d(s): 3,34,492,499,511,553 WARNING @ Tue, 16 Jun 2020 08:09:37: #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 08:09:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:09:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234910/SRX234910.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 0 millis CompletedMACS2peakCalling