Job ID = 6497427 SRX = SRX494839 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:59:42 prefetch.2.10.7: 1) Downloading 'SRR1198371'... 2020-06-25T21:59:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:02:04 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:02:04 prefetch.2.10.7: 1) 'SRR1198371' was downloaded successfully Read 21381473 spots for SRR1198371/SRR1198371.sra Written 21381473 spots for SRR1198371/SRR1198371.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: 00:05:06 21381473 reads; of these: 21381473 (100.00%) were unpaired; of these: 3814468 (17.84%) aligned 0 times 14577926 (68.18%) aligned exactly 1 time 2989079 (13.98%) aligned >1 times 82.16% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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] 4809389 / 17567005 = 0.2738 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 07:13:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.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 07:13:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:13:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:13:31: 1000000 INFO @ Fri, 26 Jun 2020 07:13:38: 2000000 INFO @ Fri, 26 Jun 2020 07:13:44: 3000000 INFO @ Fri, 26 Jun 2020 07:13:51: 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 07:13:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.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 07:13:54: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:13:54: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:13:58: 5000000 INFO @ Fri, 26 Jun 2020 07:14:01: 1000000 INFO @ Fri, 26 Jun 2020 07:14:06: 6000000 INFO @ Fri, 26 Jun 2020 07:14:08: 2000000 INFO @ Fri, 26 Jun 2020 07:14:13: 7000000 INFO @ Fri, 26 Jun 2020 07:14:15: 3000000 INFO @ Fri, 26 Jun 2020 07:14:21: 8000000 INFO @ Fri, 26 Jun 2020 07:14:22: 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 @ Fri, 26 Jun 2020 07:14:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.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 07:14:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:14:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:14:28: 9000000 INFO @ Fri, 26 Jun 2020 07:14:29: 5000000 INFO @ Fri, 26 Jun 2020 07:14:31: 1000000 INFO @ Fri, 26 Jun 2020 07:14:36: 10000000 INFO @ Fri, 26 Jun 2020 07:14:36: 6000000 INFO @ Fri, 26 Jun 2020 07:14:39: 2000000 INFO @ Fri, 26 Jun 2020 07:14:43: 11000000 INFO @ Fri, 26 Jun 2020 07:14:44: 7000000 INFO @ Fri, 26 Jun 2020 07:14:46: 3000000 INFO @ Fri, 26 Jun 2020 07:14:50: 12000000 INFO @ Fri, 26 Jun 2020 07:14:51: 8000000 INFO @ Fri, 26 Jun 2020 07:14:53: 4000000 INFO @ Fri, 26 Jun 2020 07:14:56: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:14:56: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:14:56: #1 total tags in treatment: 12757616 INFO @ Fri, 26 Jun 2020 07:14:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:14:56: #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 07:14:56: #1 tags after filtering in treatment: 12757616 INFO @ Fri, 26 Jun 2020 07:14:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:14:56: #1 finished! INFO @ Fri, 26 Jun 2020 07:14:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:14:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:14:57: #2 number of paired peaks: 339 WARNING @ Fri, 26 Jun 2020 07:14:57: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Fri, 26 Jun 2020 07:14:57: start model_add_line... INFO @ Fri, 26 Jun 2020 07:14:57: start X-correlation... INFO @ Fri, 26 Jun 2020 07:14:57: end of X-cor INFO @ Fri, 26 Jun 2020 07:14:57: #2 finished! INFO @ Fri, 26 Jun 2020 07:14:57: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 07:14:57: #2 alternative fragment length(s) may be 2,47,562 bps INFO @ Fri, 26 Jun 2020 07:14:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.05_model.r WARNING @ Fri, 26 Jun 2020 07:14:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:14:57: #2 You may need to consider one of the other alternative d(s): 2,47,562 WARNING @ Fri, 26 Jun 2020 07:14:57: #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 07:14:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:14:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:14:58: 9000000 INFO @ Fri, 26 Jun 2020 07:15:00: 5000000 INFO @ Fri, 26 Jun 2020 07:15:05: 10000000 INFO @ Fri, 26 Jun 2020 07:15:07: 6000000 INFO @ Fri, 26 Jun 2020 07:15:12: 11000000 INFO @ Fri, 26 Jun 2020 07:15:14: 7000000 INFO @ Fri, 26 Jun 2020 07:15:18: 12000000 INFO @ Fri, 26 Jun 2020 07:15:20: 8000000 INFO @ Fri, 26 Jun 2020 07:15:20: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:15:23: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:15:23: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:15:23: #1 total tags in treatment: 12757616 INFO @ Fri, 26 Jun 2020 07:15:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:15:23: #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 07:15:24: #1 tags after filtering in treatment: 12757616 INFO @ Fri, 26 Jun 2020 07:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:15:24: #1 finished! INFO @ Fri, 26 Jun 2020 07:15:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:15:24: #2 number of paired peaks: 339 WARNING @ Fri, 26 Jun 2020 07:15:24: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Fri, 26 Jun 2020 07:15:24: start model_add_line... INFO @ Fri, 26 Jun 2020 07:15:25: start X-correlation... INFO @ Fri, 26 Jun 2020 07:15:25: end of X-cor INFO @ Fri, 26 Jun 2020 07:15:25: #2 finished! INFO @ Fri, 26 Jun 2020 07:15:25: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 07:15:25: #2 alternative fragment length(s) may be 2,47,562 bps INFO @ Fri, 26 Jun 2020 07:15:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.10_model.r WARNING @ Fri, 26 Jun 2020 07:15:25: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:15:25: #2 You may need to consider one of the other alternative d(s): 2,47,562 WARNING @ Fri, 26 Jun 2020 07:15:25: #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 07:15:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:15:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:15:27: 9000000 INFO @ Fri, 26 Jun 2020 07:15:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:15:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:15:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.05_summits.bed INFO @ Fri, 26 Jun 2020 07:15:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (753 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:15:33: 10000000 INFO @ Fri, 26 Jun 2020 07:15:39: 11000000 INFO @ Fri, 26 Jun 2020 07:15:46: 12000000 INFO @ Fri, 26 Jun 2020 07:15:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:15:50: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:15:50: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:15:50: #1 total tags in treatment: 12757616 INFO @ Fri, 26 Jun 2020 07:15:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:15:50: #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 07:15:50: #1 tags after filtering in treatment: 12757616 INFO @ Fri, 26 Jun 2020 07:15:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:15:50: #1 finished! INFO @ Fri, 26 Jun 2020 07:15:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:15:51: #2 number of paired peaks: 339 WARNING @ Fri, 26 Jun 2020 07:15:51: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Fri, 26 Jun 2020 07:15:51: start model_add_line... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:15:51: start X-correlation... INFO @ Fri, 26 Jun 2020 07:15:51: end of X-cor INFO @ Fri, 26 Jun 2020 07:15:51: #2 finished! INFO @ Fri, 26 Jun 2020 07:15:51: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 07:15:51: #2 alternative fragment length(s) may be 2,47,562 bps INFO @ Fri, 26 Jun 2020 07:15:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.20_model.r WARNING @ Fri, 26 Jun 2020 07:15:51: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:15:51: #2 You may need to consider one of the other alternative d(s): 2,47,562 WARNING @ Fri, 26 Jun 2020 07:15:51: #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 07:15:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:15:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.10_summits.bed INFO @ Fri, 26 Jun 2020 07:16:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (470 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:16:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:16:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:16:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:16:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494839/SRX494839.20_summits.bed INFO @ Fri, 26 Jun 2020 07:16:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 1 millis CompletedMACS2peakCalling