Job ID = 6497412 SRX = SRX494824 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:04:58 prefetch.2.10.7: 1) Downloading 'SRR1198356'... 2020-06-25T22:04:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:06:34 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:06:35 prefetch.2.10.7: 'SRR1198356' is valid 2020-06-25T22:06:35 prefetch.2.10.7: 1) 'SRR1198356' was downloaded successfully Read 16299342 spots for SRR1198356/SRR1198356.sra Written 16299342 spots for SRR1198356/SRR1198356.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: 00:00:01 Multiseed full-index search: 00:02:35 16299342 reads; of these: 16299342 (100.00%) were unpaired; of these: 3611808 (22.16%) aligned 0 times 10553910 (64.75%) aligned exactly 1 time 2133624 (13.09%) aligned >1 times 77.84% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 1071245 / 12687534 = 0.0844 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 07:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.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 07:13:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:13:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:13:24: 1000000 INFO @ Fri, 26 Jun 2020 07:13:30: 2000000 INFO @ Fri, 26 Jun 2020 07:13:36: 3000000 INFO @ Fri, 26 Jun 2020 07:13:42: 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 07:13:47: 5000000 INFO @ Fri, 26 Jun 2020 07:13:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.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 07:13:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:13:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:13:54: 6000000 INFO @ Fri, 26 Jun 2020 07:13:55: 1000000 INFO @ Fri, 26 Jun 2020 07:14:00: 7000000 INFO @ Fri, 26 Jun 2020 07:14:02: 2000000 INFO @ Fri, 26 Jun 2020 07:14:06: 8000000 INFO @ Fri, 26 Jun 2020 07:14:09: 3000000 INFO @ Fri, 26 Jun 2020 07:14:13: 9000000 INFO @ Fri, 26 Jun 2020 07:14:16: 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 07:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.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 07:14:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:14:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:14:19: 10000000 INFO @ Fri, 26 Jun 2020 07:14:23: 5000000 INFO @ Fri, 26 Jun 2020 07:14:25: 11000000 INFO @ Fri, 26 Jun 2020 07:14:26: 1000000 INFO @ Fri, 26 Jun 2020 07:14:29: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:14:29: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:14:29: #1 total tags in treatment: 11616289 INFO @ Fri, 26 Jun 2020 07:14:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:14:29: #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 07:14:29: #1 tags after filtering in treatment: 11616289 INFO @ Fri, 26 Jun 2020 07:14:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:14:29: #1 finished! INFO @ Fri, 26 Jun 2020 07:14:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:14:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:14:30: 6000000 INFO @ Fri, 26 Jun 2020 07:14:30: #2 number of paired peaks: 342 WARNING @ Fri, 26 Jun 2020 07:14:30: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Fri, 26 Jun 2020 07:14:30: start model_add_line... INFO @ Fri, 26 Jun 2020 07:14:30: start X-correlation... INFO @ Fri, 26 Jun 2020 07:14:30: end of X-cor INFO @ Fri, 26 Jun 2020 07:14:30: #2 finished! INFO @ Fri, 26 Jun 2020 07:14:30: #2 predicted fragment length is 33 bps INFO @ Fri, 26 Jun 2020 07:14:30: #2 alternative fragment length(s) may be 2,33,559 bps INFO @ Fri, 26 Jun 2020 07:14:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.05_model.r WARNING @ Fri, 26 Jun 2020 07:14:30: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:14:30: #2 You may need to consider one of the other alternative d(s): 2,33,559 WARNING @ Fri, 26 Jun 2020 07:14:30: #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 07:14:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:14:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:14:33: 2000000 INFO @ Fri, 26 Jun 2020 07:14:36: 7000000 INFO @ Fri, 26 Jun 2020 07:14:40: 3000000 INFO @ Fri, 26 Jun 2020 07:14:43: 8000000 INFO @ Fri, 26 Jun 2020 07:14:47: 4000000 INFO @ Fri, 26 Jun 2020 07:14:50: 9000000 INFO @ Fri, 26 Jun 2020 07:14:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:14:54: 5000000 INFO @ Fri, 26 Jun 2020 07:14:57: 10000000 INFO @ Fri, 26 Jun 2020 07:15:01: 6000000 INFO @ Fri, 26 Jun 2020 07:15:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:15:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:15:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.05_summits.bed INFO @ Fri, 26 Jun 2020 07:15:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (696 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:15:04: 11000000 INFO @ Fri, 26 Jun 2020 07:15:07: 7000000 INFO @ Fri, 26 Jun 2020 07:15:08: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:15:08: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:15:08: #1 total tags in treatment: 11616289 INFO @ Fri, 26 Jun 2020 07:15:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:15:08: #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 07:15:08: #1 tags after filtering in treatment: 11616289 INFO @ Fri, 26 Jun 2020 07:15:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:15:08: #1 finished! INFO @ Fri, 26 Jun 2020 07:15:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:15:09: #2 number of paired peaks: 342 WARNING @ Fri, 26 Jun 2020 07:15:09: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Fri, 26 Jun 2020 07:15:09: start model_add_line... INFO @ Fri, 26 Jun 2020 07:15:09: start X-correlation... INFO @ Fri, 26 Jun 2020 07:15:09: end of X-cor INFO @ Fri, 26 Jun 2020 07:15:09: #2 finished! INFO @ Fri, 26 Jun 2020 07:15:09: #2 predicted fragment length is 33 bps INFO @ Fri, 26 Jun 2020 07:15:09: #2 alternative fragment length(s) may be 2,33,559 bps INFO @ Fri, 26 Jun 2020 07:15:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.10_model.r WARNING @ Fri, 26 Jun 2020 07:15:09: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:15:09: #2 You may need to consider one of the other alternative d(s): 2,33,559 WARNING @ Fri, 26 Jun 2020 07:15:09: #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 07:15:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:15:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:15:14: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:15:20: 9000000 INFO @ Fri, 26 Jun 2020 07:15:26: 10000000 INFO @ Fri, 26 Jun 2020 07:15:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:15:32: 11000000 INFO @ Fri, 26 Jun 2020 07:15:36: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:15:36: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:15:36: #1 total tags in treatment: 11616289 INFO @ Fri, 26 Jun 2020 07:15:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:15:36: #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 07:15:36: #1 tags after filtering in treatment: 11616289 INFO @ Fri, 26 Jun 2020 07:15:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:15:36: #1 finished! INFO @ Fri, 26 Jun 2020 07:15:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:15:37: #2 number of paired peaks: 342 WARNING @ Fri, 26 Jun 2020 07:15:37: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Fri, 26 Jun 2020 07:15:37: start model_add_line... INFO @ Fri, 26 Jun 2020 07:15:37: start X-correlation... INFO @ Fri, 26 Jun 2020 07:15:37: end of X-cor INFO @ Fri, 26 Jun 2020 07:15:37: #2 finished! INFO @ Fri, 26 Jun 2020 07:15:37: #2 predicted fragment length is 33 bps INFO @ Fri, 26 Jun 2020 07:15:37: #2 alternative fragment length(s) may be 2,33,559 bps INFO @ Fri, 26 Jun 2020 07:15:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.20_model.r WARNING @ Fri, 26 Jun 2020 07:15:37: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:15:37: #2 You may need to consider one of the other alternative d(s): 2,33,559 WARNING @ Fri, 26 Jun 2020 07:15:37: #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 07:15:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:15:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:15:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:15:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:15:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.10_summits.bed INFO @ Fri, 26 Jun 2020 07:15:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (318 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:15:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:16:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:16:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:16:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494824/SRX494824.20_summits.bed INFO @ Fri, 26 Jun 2020 07:16:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (96 records, 4 fields): 1 millis CompletedMACS2peakCalling