Job ID = 6508000 SRX = SRX743650 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:39:12 prefetch.2.10.7: 1) Downloading 'SRR1630865'... 2020-06-26T13:39:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:41:29 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:41:30 prefetch.2.10.7: 'SRR1630865' is valid 2020-06-26T13:41:30 prefetch.2.10.7: 1) 'SRR1630865' was downloaded successfully Read 14530482 spots for SRR1630865/SRR1630865.sra Written 14530482 spots for SRR1630865/SRR1630865.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:19 14530482 reads; of these: 14530482 (100.00%) were unpaired; of these: 3145850 (21.65%) aligned 0 times 9766877 (67.22%) aligned exactly 1 time 1617755 (11.13%) aligned >1 times 78.35% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 1195019 / 11384632 = 0.1050 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 @ Fri, 26 Jun 2020 22:49:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.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 @ Fri, 26 Jun 2020 22:49:04: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:49:04: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:49:10: 1000000 INFO @ Fri, 26 Jun 2020 22:49:16: 2000000 INFO @ Fri, 26 Jun 2020 22:49:21: 3000000 INFO @ Fri, 26 Jun 2020 22:49:27: 4000000 INFO @ Fri, 26 Jun 2020 22:49:32: 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 @ Fri, 26 Jun 2020 22:49:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.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 @ Fri, 26 Jun 2020 22:49:34: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:49:34: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:49:38: 6000000 INFO @ Fri, 26 Jun 2020 22:49:40: 1000000 INFO @ Fri, 26 Jun 2020 22:49:44: 7000000 INFO @ Fri, 26 Jun 2020 22:49:47: 2000000 INFO @ Fri, 26 Jun 2020 22:49:50: 8000000 INFO @ Fri, 26 Jun 2020 22:49:53: 3000000 INFO @ Fri, 26 Jun 2020 22:49:56: 9000000 INFO @ Fri, 26 Jun 2020 22:49:59: 4000000 BedGraph に変換中... INFO @ Fri, 26 Jun 2020 22:50:03: 10000000 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 @ Fri, 26 Jun 2020 22:50:04: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 22:50:04: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 22:50:04: #1 total tags in treatment: 10189613 INFO @ Fri, 26 Jun 2020 22:50:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:50:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:50:04: #1 tags after filtering in treatment: 10189613 INFO @ Fri, 26 Jun 2020 22:50:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:50:04: #1 finished! INFO @ Fri, 26 Jun 2020 22:50:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:50:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:50:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.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 @ Fri, 26 Jun 2020 22:50:04: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:50:04: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:50:05: #2 number of paired peaks: 164 WARNING @ Fri, 26 Jun 2020 22:50:05: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 26 Jun 2020 22:50:05: start model_add_line... INFO @ Fri, 26 Jun 2020 22:50:05: start X-correlation... INFO @ Fri, 26 Jun 2020 22:50:05: end of X-cor INFO @ Fri, 26 Jun 2020 22:50:05: #2 finished! INFO @ Fri, 26 Jun 2020 22:50:05: #2 predicted fragment length is 54 bps INFO @ Fri, 26 Jun 2020 22:50:05: #2 alternative fragment length(s) may be 2,54,525,571 bps INFO @ Fri, 26 Jun 2020 22:50:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.05_model.r WARNING @ Fri, 26 Jun 2020 22:50:05: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:50:05: #2 You may need to consider one of the other alternative d(s): 2,54,525,571 WARNING @ Fri, 26 Jun 2020 22:50:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:50:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:50:05: 5000000 INFO @ Fri, 26 Jun 2020 22:50:11: 1000000 INFO @ Fri, 26 Jun 2020 22:50:11: 6000000 INFO @ Fri, 26 Jun 2020 22:50:17: 2000000 INFO @ Fri, 26 Jun 2020 22:50:17: 7000000 INFO @ Fri, 26 Jun 2020 22:50:23: 3000000 INFO @ Fri, 26 Jun 2020 22:50:23: 8000000 INFO @ Fri, 26 Jun 2020 22:50:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:50:29: 4000000 INFO @ Fri, 26 Jun 2020 22:50:29: 9000000 INFO @ Fri, 26 Jun 2020 22:50:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:50:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:50:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.05_summits.bed INFO @ Fri, 26 Jun 2020 22:50:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (497 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:50:35: 5000000 INFO @ Fri, 26 Jun 2020 22:50:35: 10000000 INFO @ Fri, 26 Jun 2020 22:50:36: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 22:50:36: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 22:50:36: #1 total tags in treatment: 10189613 INFO @ Fri, 26 Jun 2020 22:50:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:50:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:50:36: #1 tags after filtering in treatment: 10189613 INFO @ Fri, 26 Jun 2020 22:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:50:36: #1 finished! INFO @ Fri, 26 Jun 2020 22:50:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:50:37: #2 number of paired peaks: 164 WARNING @ Fri, 26 Jun 2020 22:50:37: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 26 Jun 2020 22:50:37: start model_add_line... INFO @ Fri, 26 Jun 2020 22:50:37: start X-correlation... INFO @ Fri, 26 Jun 2020 22:50:37: end of X-cor INFO @ Fri, 26 Jun 2020 22:50:37: #2 finished! INFO @ Fri, 26 Jun 2020 22:50:37: #2 predicted fragment length is 54 bps INFO @ Fri, 26 Jun 2020 22:50:37: #2 alternative fragment length(s) may be 2,54,525,571 bps INFO @ Fri, 26 Jun 2020 22:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.10_model.r WARNING @ Fri, 26 Jun 2020 22:50:37: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:50:37: #2 You may need to consider one of the other alternative d(s): 2,54,525,571 WARNING @ Fri, 26 Jun 2020 22:50:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:50:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:50:41: 6000000 INFO @ Fri, 26 Jun 2020 22:50:47: 7000000 INFO @ Fri, 26 Jun 2020 22:50:52: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:50:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:50:58: 9000000 INFO @ Fri, 26 Jun 2020 22:51:04: 10000000 INFO @ Fri, 26 Jun 2020 22:51:05: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 22:51:05: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 22:51:05: #1 total tags in treatment: 10189613 INFO @ Fri, 26 Jun 2020 22:51:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:51:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:51:05: #1 tags after filtering in treatment: 10189613 INFO @ Fri, 26 Jun 2020 22:51:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:51:05: #1 finished! INFO @ Fri, 26 Jun 2020 22:51:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:51:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:51:06: #2 number of paired peaks: 164 WARNING @ Fri, 26 Jun 2020 22:51:06: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 26 Jun 2020 22:51:06: start model_add_line... INFO @ Fri, 26 Jun 2020 22:51:06: start X-correlation... INFO @ Fri, 26 Jun 2020 22:51:06: end of X-cor INFO @ Fri, 26 Jun 2020 22:51:06: #2 finished! INFO @ Fri, 26 Jun 2020 22:51:06: #2 predicted fragment length is 54 bps INFO @ Fri, 26 Jun 2020 22:51:06: #2 alternative fragment length(s) may be 2,54,525,571 bps INFO @ Fri, 26 Jun 2020 22:51:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.20_model.r WARNING @ Fri, 26 Jun 2020 22:51:06: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:51:06: #2 You may need to consider one of the other alternative d(s): 2,54,525,571 WARNING @ Fri, 26 Jun 2020 22:51:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:51:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:51:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:51:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:51:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:51:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.10_summits.bed INFO @ Fri, 26 Jun 2020 22:51:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (252 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:51:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:51:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:51:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:51:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX743650/SRX743650.20_summits.bed INFO @ Fri, 26 Jun 2020 22:51:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (92 records, 4 fields): 2 millis CompletedMACS2peakCalling