Job ID = 6497469 SRX = SRX494970 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:00:57 prefetch.2.10.7: 1) Downloading 'SRR1198502'... 2020-06-25T22:00:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:03:18 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:03:19 prefetch.2.10.7: 'SRR1198502' is valid 2020-06-25T22:03:19 prefetch.2.10.7: 1) 'SRR1198502' was downloaded successfully Read 19040559 spots for SRR1198502/SRR1198502.sra Written 19040559 spots for SRR1198502/SRR1198502.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: 00:04:21 19040559 reads; of these: 19040559 (100.00%) were unpaired; of these: 793926 (4.17%) aligned 0 times 15280174 (80.25%) aligned exactly 1 time 2966459 (15.58%) aligned >1 times 95.83% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 10943387 / 18246633 = 0.5997 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 07:12:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.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 07:12:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:12:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:12:13: 1000000 INFO @ Fri, 26 Jun 2020 07:12:18: 2000000 INFO @ Fri, 26 Jun 2020 07:12:23: 3000000 INFO @ Fri, 26 Jun 2020 07:12:27: 4000000 INFO @ Fri, 26 Jun 2020 07:12:32: 5000000 INFO @ Fri, 26 Jun 2020 07:12:37: 6000000 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 07:12:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.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 07:12:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:12:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:12:41: 7000000 INFO @ Fri, 26 Jun 2020 07:12:43: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:12:43: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:12:43: #1 total tags in treatment: 7303246 INFO @ Fri, 26 Jun 2020 07:12:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:12:43: #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 07:12:43: #1 tags after filtering in treatment: 7303246 INFO @ Fri, 26 Jun 2020 07:12:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:12:43: #1 finished! INFO @ Fri, 26 Jun 2020 07:12:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:12:44: 1000000 INFO @ Fri, 26 Jun 2020 07:12:44: #2 number of paired peaks: 499 WARNING @ Fri, 26 Jun 2020 07:12:44: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Fri, 26 Jun 2020 07:12:44: start model_add_line... INFO @ Fri, 26 Jun 2020 07:12:44: start X-correlation... INFO @ Fri, 26 Jun 2020 07:12:44: end of X-cor INFO @ Fri, 26 Jun 2020 07:12:44: #2 finished! INFO @ Fri, 26 Jun 2020 07:12:44: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 07:12:44: #2 alternative fragment length(s) may be 3,47,561 bps INFO @ Fri, 26 Jun 2020 07:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.05_model.r WARNING @ Fri, 26 Jun 2020 07:12:44: #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 07:12:44: #2 You may need to consider one of the other alternative d(s): 3,47,561 WARNING @ Fri, 26 Jun 2020 07:12:44: #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 07:12:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:12:48: 2000000 INFO @ Fri, 26 Jun 2020 07:12:53: 3000000 INFO @ Fri, 26 Jun 2020 07:12:58: 4000000 INFO @ Fri, 26 Jun 2020 07:12:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:13:03: 5000000 INFO @ Fri, 26 Jun 2020 07:13:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:13:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:13:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.05_summits.bed INFO @ Fri, 26 Jun 2020 07:13:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (784 records, 4 fields): 2 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 @ Fri, 26 Jun 2020 07:13:07: 6000000 INFO @ Fri, 26 Jun 2020 07:13:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.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 07:13:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:13:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:13:12: 7000000 INFO @ Fri, 26 Jun 2020 07:13:14: 1000000 INFO @ Fri, 26 Jun 2020 07:13:14: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:13:14: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:13:14: #1 total tags in treatment: 7303246 INFO @ Fri, 26 Jun 2020 07:13:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:13:14: #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 07:13:14: #1 tags after filtering in treatment: 7303246 INFO @ Fri, 26 Jun 2020 07:13:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:13:14: #1 finished! INFO @ Fri, 26 Jun 2020 07:13:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:13:14: #2 number of paired peaks: 499 WARNING @ Fri, 26 Jun 2020 07:13:14: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Fri, 26 Jun 2020 07:13:14: start model_add_line... INFO @ Fri, 26 Jun 2020 07:13:14: start X-correlation... INFO @ Fri, 26 Jun 2020 07:13:14: end of X-cor INFO @ Fri, 26 Jun 2020 07:13:14: #2 finished! INFO @ Fri, 26 Jun 2020 07:13:14: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 07:13:14: #2 alternative fragment length(s) may be 3,47,561 bps INFO @ Fri, 26 Jun 2020 07:13:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.10_model.r INFO @ Fri, 26 Jun 2020 07:13:18: 2000000 INFO @ Fri, 26 Jun 2020 07:13:23: 3000000 WARNING @ Fri, 26 Jun 2020 07:13:23: #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 07:13:23: #2 You may need to consider one of the other alternative d(s): 3,47,561 WARNING @ Fri, 26 Jun 2020 07:13:23: #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 07:13:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:13:28: 4000000 INFO @ Fri, 26 Jun 2020 07:13:33: 5000000 INFO @ Fri, 26 Jun 2020 07:13:37: 6000000 INFO @ Fri, 26 Jun 2020 07:13:39: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:13:42: 7000000 INFO @ Fri, 26 Jun 2020 07:13:43: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:13:43: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:13:43: #1 total tags in treatment: 7303246 INFO @ Fri, 26 Jun 2020 07:13:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:13:43: #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 07:13:44: #1 tags after filtering in treatment: 7303246 INFO @ Fri, 26 Jun 2020 07:13:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:13:44: #1 finished! INFO @ Fri, 26 Jun 2020 07:13:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:13:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:13:44: #2 number of paired peaks: 499 WARNING @ Fri, 26 Jun 2020 07:13:44: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Fri, 26 Jun 2020 07:13:44: start model_add_line... INFO @ Fri, 26 Jun 2020 07:13:44: start X-correlation... INFO @ Fri, 26 Jun 2020 07:13:44: end of X-cor INFO @ Fri, 26 Jun 2020 07:13:44: #2 finished! INFO @ Fri, 26 Jun 2020 07:13:44: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 07:13:44: #2 alternative fragment length(s) may be 3,47,561 bps INFO @ Fri, 26 Jun 2020 07:13:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.20_model.r WARNING @ Fri, 26 Jun 2020 07:13:45: #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 07:13:45: #2 You may need to consider one of the other alternative d(s): 3,47,561 WARNING @ Fri, 26 Jun 2020 07:13:45: #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 07:13:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:13:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:13:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:13:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:13:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.10_summits.bed INFO @ Fri, 26 Jun 2020 07:13:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (569 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:14:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:14:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:14:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:14:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494970/SRX494970.20_summits.bed INFO @ Fri, 26 Jun 2020 07:14:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (232 records, 4 fields): 1 millis CompletedMACS2peakCalling