Job ID = 6497567 SRX = SRX743650 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:01:25 prefetch.2.10.7: 1) Downloading 'SRR1630865'... 2020-06-25T22:01:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:03:06 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:03:07 prefetch.2.10.7: 'SRR1630865' is valid 2020-06-25T22:03:07 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:29 14530482 reads; of these: 14530482 (100.00%) were unpaired; of these: 3146681 (21.66%) aligned 0 times 9766105 (67.21%) aligned exactly 1 time 1617696 (11.13%) aligned >1 times 78.34% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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] 1194815 / 11383801 = 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 07:11:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:11:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:11:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:11:54: 1000000 INFO @ Fri, 26 Jun 2020 07:12:01: 2000000 INFO @ Fri, 26 Jun 2020 07:12:07: 3000000 INFO @ Fri, 26 Jun 2020 07:12:14: 4000000 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 07:12:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:12:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:12:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:12:22: 5000000 INFO @ Fri, 26 Jun 2020 07:12:24: 1000000 INFO @ Fri, 26 Jun 2020 07:12:29: 6000000 INFO @ Fri, 26 Jun 2020 07:12:31: 2000000 INFO @ Fri, 26 Jun 2020 07:12:36: 7000000 INFO @ Fri, 26 Jun 2020 07:12:38: 3000000 INFO @ Fri, 26 Jun 2020 07:12:43: 8000000 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 @ Fri, 26 Jun 2020 07:12:46: 4000000 INFO @ Fri, 26 Jun 2020 07:12:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:12:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:12:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:12:50: 9000000 INFO @ Fri, 26 Jun 2020 07:12:53: 5000000 INFO @ Fri, 26 Jun 2020 07:12:54: 1000000 INFO @ Fri, 26 Jun 2020 07:12:58: 10000000 INFO @ Fri, 26 Jun 2020 07:12:59: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 07:12:59: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 07:12:59: #1 total tags in treatment: 10188986 INFO @ Fri, 26 Jun 2020 07:12:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:12:59: #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 07:12:59: #1 tags after filtering in treatment: 10188986 INFO @ Fri, 26 Jun 2020 07:12:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:12:59: #1 finished! INFO @ Fri, 26 Jun 2020 07:12:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:12:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:13:00: #2 number of paired peaks: 163 WARNING @ Fri, 26 Jun 2020 07:13:00: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Fri, 26 Jun 2020 07:13:00: start model_add_line... INFO @ Fri, 26 Jun 2020 07:13:00: start X-correlation... INFO @ Fri, 26 Jun 2020 07:13:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:13:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:13:00: #2 predicted fragment length is 54 bps INFO @ Fri, 26 Jun 2020 07:13:00: #2 alternative fragment length(s) may be 2,54,525,566 bps INFO @ Fri, 26 Jun 2020 07:13:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.05_model.r WARNING @ Fri, 26 Jun 2020 07:13:00: #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 07:13:00: #2 You may need to consider one of the other alternative d(s): 2,54,525,566 WARNING @ Fri, 26 Jun 2020 07:13:00: #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 07:13:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:13:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:13:01: 6000000 INFO @ Fri, 26 Jun 2020 07:13:02: 2000000 INFO @ Fri, 26 Jun 2020 07:13:08: 7000000 INFO @ Fri, 26 Jun 2020 07:13:09: 3000000 INFO @ Fri, 26 Jun 2020 07:13:15: 8000000 INFO @ Fri, 26 Jun 2020 07:13:17: 4000000 INFO @ Fri, 26 Jun 2020 07:13:20: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:13:23: 9000000 INFO @ Fri, 26 Jun 2020 07:13:24: 5000000 INFO @ Fri, 26 Jun 2020 07:13:30: 10000000 INFO @ Fri, 26 Jun 2020 07:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.05_summits.bed INFO @ Fri, 26 Jun 2020 07:13:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (495 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:13:31: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 07:13:31: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 07:13:31: #1 total tags in treatment: 10188986 INFO @ Fri, 26 Jun 2020 07:13:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:13:31: #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 07:13:31: #1 tags after filtering in treatment: 10188986 INFO @ Fri, 26 Jun 2020 07:13:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:13:31: #1 finished! INFO @ Fri, 26 Jun 2020 07:13:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:13:32: #2 number of paired peaks: 163 WARNING @ Fri, 26 Jun 2020 07:13:32: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Fri, 26 Jun 2020 07:13:32: start model_add_line... INFO @ Fri, 26 Jun 2020 07:13:32: start X-correlation... INFO @ Fri, 26 Jun 2020 07:13:32: end of X-cor INFO @ Fri, 26 Jun 2020 07:13:32: #2 finished! INFO @ Fri, 26 Jun 2020 07:13:32: #2 predicted fragment length is 54 bps INFO @ Fri, 26 Jun 2020 07:13:32: #2 alternative fragment length(s) may be 2,54,525,566 bps INFO @ Fri, 26 Jun 2020 07:13:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.10_model.r WARNING @ Fri, 26 Jun 2020 07:13:32: #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 07:13:32: #2 You may need to consider one of the other alternative d(s): 2,54,525,566 WARNING @ Fri, 26 Jun 2020 07:13:32: #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 07:13:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:13:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:13:32: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:13:39: 7000000 INFO @ Fri, 26 Jun 2020 07:13:46: 8000000 INFO @ Fri, 26 Jun 2020 07:13:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:13:53: 9000000 INFO @ Fri, 26 Jun 2020 07:14:00: 10000000 INFO @ Fri, 26 Jun 2020 07:14:01: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 07:14:01: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 07:14:01: #1 total tags in treatment: 10188986 INFO @ Fri, 26 Jun 2020 07:14:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:14:01: #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 07:14:01: #1 tags after filtering in treatment: 10188986 INFO @ Fri, 26 Jun 2020 07:14:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:14:01: #1 finished! INFO @ Fri, 26 Jun 2020 07:14:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:14:02: #2 number of paired peaks: 163 WARNING @ Fri, 26 Jun 2020 07:14:02: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Fri, 26 Jun 2020 07:14:02: start model_add_line... INFO @ Fri, 26 Jun 2020 07:14:02: start X-correlation... INFO @ Fri, 26 Jun 2020 07:14:02: end of X-cor INFO @ Fri, 26 Jun 2020 07:14:02: #2 finished! INFO @ Fri, 26 Jun 2020 07:14:02: #2 predicted fragment length is 54 bps INFO @ Fri, 26 Jun 2020 07:14:02: #2 alternative fragment length(s) may be 2,54,525,566 bps INFO @ Fri, 26 Jun 2020 07:14:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.20_model.r WARNING @ Fri, 26 Jun 2020 07:14:02: #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 07:14:02: #2 You may need to consider one of the other alternative d(s): 2,54,525,566 WARNING @ Fri, 26 Jun 2020 07:14:02: #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 07:14:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:14:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:14:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:14:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:14:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.10_summits.bed INFO @ Fri, 26 Jun 2020 07:14:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (249 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:14:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:14:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:14:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:14:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX743650/SRX743650.20_summits.bed INFO @ Fri, 26 Jun 2020 07:14:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (93 records, 4 fields): 28 millis CompletedMACS2peakCalling