Job ID = 6497461 SRX = SRX494962 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:14:44 prefetch.2.10.7: 1) Downloading 'SRR1198494'... 2020-06-25T22:14:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:15:58 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:15:59 prefetch.2.10.7: 'SRR1198494' is valid 2020-06-25T22:15:59 prefetch.2.10.7: 1) 'SRR1198494' was downloaded successfully Read 13129788 spots for SRR1198494/SRR1198494.sra Written 13129788 spots for SRR1198494/SRR1198494.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: 00:03:04 13129788 reads; of these: 13129788 (100.00%) were unpaired; of these: 270410 (2.06%) aligned 0 times 10628242 (80.95%) aligned exactly 1 time 2231136 (16.99%) aligned >1 times 97.94% overall alignment rate Time searching: 00:03:04 Overall time: 00:03:04 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] 2050920 / 12859378 = 0.1595 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 07:22:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.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 07:22:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:22:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:22:48: 1000000 INFO @ Fri, 26 Jun 2020 07:22:54: 2000000 INFO @ Fri, 26 Jun 2020 07:23:00: 3000000 INFO @ Fri, 26 Jun 2020 07:23:06: 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 07:23:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.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 07:23:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:23:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:23:12: 5000000 INFO @ Fri, 26 Jun 2020 07:23:18: 1000000 INFO @ Fri, 26 Jun 2020 07:23:18: 6000000 INFO @ Fri, 26 Jun 2020 07:23:25: 2000000 INFO @ Fri, 26 Jun 2020 07:23:25: 7000000 INFO @ Fri, 26 Jun 2020 07:23:31: 3000000 INFO @ Fri, 26 Jun 2020 07:23:31: 8000000 INFO @ Fri, 26 Jun 2020 07:23:38: 4000000 INFO @ Fri, 26 Jun 2020 07:23:38: 9000000 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 07:23:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.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 07:23:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:23:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:23:45: 10000000 INFO @ Fri, 26 Jun 2020 07:23:45: 5000000 INFO @ Fri, 26 Jun 2020 07:23:49: 1000000 INFO @ Fri, 26 Jun 2020 07:23:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:23:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:23:51: #1 total tags in treatment: 10808458 INFO @ Fri, 26 Jun 2020 07:23:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:23:51: #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 07:23:51: #1 tags after filtering in treatment: 10808458 INFO @ Fri, 26 Jun 2020 07:23:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:23:51: #1 finished! INFO @ Fri, 26 Jun 2020 07:23:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:23:52: #2 number of paired peaks: 384 WARNING @ Fri, 26 Jun 2020 07:23:52: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Fri, 26 Jun 2020 07:23:52: start model_add_line... INFO @ Fri, 26 Jun 2020 07:23:52: start X-correlation... INFO @ Fri, 26 Jun 2020 07:23:52: end of X-cor INFO @ Fri, 26 Jun 2020 07:23:52: #2 finished! INFO @ Fri, 26 Jun 2020 07:23:52: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 07:23:52: #2 alternative fragment length(s) may be 2,46,568,571 bps INFO @ Fri, 26 Jun 2020 07:23:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.05_model.r INFO @ Fri, 26 Jun 2020 07:23:52: 6000000 INFO @ Fri, 26 Jun 2020 07:23:57: 2000000 INFO @ Fri, 26 Jun 2020 07:24:00: 7000000 INFO @ Fri, 26 Jun 2020 07:24:05: 3000000 INFO @ Fri, 26 Jun 2020 07:24:07: 8000000 INFO @ Fri, 26 Jun 2020 07:24:12: 4000000 INFO @ Fri, 26 Jun 2020 07:24:14: 9000000 INFO @ Fri, 26 Jun 2020 07:24:20: 5000000 INFO @ Fri, 26 Jun 2020 07:24:21: 10000000 INFO @ Fri, 26 Jun 2020 07:24:26: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:24:26: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:24:26: #1 total tags in treatment: 10808458 INFO @ Fri, 26 Jun 2020 07:24:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:24:26: #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 07:24:26: #1 tags after filtering in treatment: 10808458 INFO @ Fri, 26 Jun 2020 07:24:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:24:26: #1 finished! INFO @ Fri, 26 Jun 2020 07:24:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:24:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:24:27: #2 number of paired peaks: 384 WARNING @ Fri, 26 Jun 2020 07:24:27: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Fri, 26 Jun 2020 07:24:27: start model_add_line... INFO @ Fri, 26 Jun 2020 07:24:27: 6000000 INFO @ Fri, 26 Jun 2020 07:24:27: start X-correlation... INFO @ Fri, 26 Jun 2020 07:24:27: end of X-cor INFO @ Fri, 26 Jun 2020 07:24:27: #2 finished! INFO @ Fri, 26 Jun 2020 07:24:27: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 07:24:27: #2 alternative fragment length(s) may be 2,46,568,571 bps INFO @ Fri, 26 Jun 2020 07:24:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.10_model.r BedGraph に変換しました。 INFO @ Fri, 26 Jun 2020 07:24:34: 7000000 INFO @ Fri, 26 Jun 2020 07:24:41: 8000000 WARNING @ Fri, 26 Jun 2020 07:24:43: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:24:43: #2 You may need to consider one of the other alternative d(s): 2,46,568,571 WARNING @ Fri, 26 Jun 2020 07:24:43: #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 07:24:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:24:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換中... WARNING @ Fri, 26 Jun 2020 07:24:43: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:24:43: #2 You may need to consider one of the other alternative d(s): 2,46,568,571 WARNING @ Fri, 26 Jun 2020 07:24:43: #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 07:24:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:24:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:24:48: 9000000 INFO @ Fri, 26 Jun 2020 07:24:55: 10000000 INFO @ Fri, 26 Jun 2020 07:25:00: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:25:00: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:25:00: #1 total tags in treatment: 10808458 INFO @ Fri, 26 Jun 2020 07:25:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:25:00: #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 07:25:00: #1 tags after filtering in treatment: 10808458 INFO @ Fri, 26 Jun 2020 07:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:25:00: #1 finished! INFO @ Fri, 26 Jun 2020 07:25:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:25:01: #2 number of paired peaks: 384 WARNING @ Fri, 26 Jun 2020 07:25:01: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Fri, 26 Jun 2020 07:25:01: start model_add_line... INFO @ Fri, 26 Jun 2020 07:25:01: start X-correlation... INFO @ Fri, 26 Jun 2020 07:25:01: end of X-cor INFO @ Fri, 26 Jun 2020 07:25:01: #2 finished! INFO @ Fri, 26 Jun 2020 07:25:01: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 07:25:01: #2 alternative fragment length(s) may be 2,46,568,571 bps INFO @ Fri, 26 Jun 2020 07:25:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.20_model.r INFO @ Fri, 26 Jun 2020 07:25:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:25:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:25:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.10_peaks.narrowPeak WARNING @ Fri, 26 Jun 2020 07:25:34: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:25:34: #2 You may need to consider one of the other alternative d(s): 2,46,568,571 WARNING @ Fri, 26 Jun 2020 07:25:34: #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 07:25:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:25:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:25:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.10_summits.bed INFO @ Fri, 26 Jun 2020 07:25:34: Done! INFO @ Fri, 26 Jun 2020 07:25:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.05_summits.bed INFO @ Fri, 26 Jun 2020 07:25:34: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 5 millis pass2 - checking and writing primary data (481 records, 4 fields): 3 millis pass1 - making usageList (7 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (691 records, 4 fields): 86 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:25:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:26:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494962/SRX494962.20_summits.bed INFO @ Fri, 26 Jun 2020 07:26:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (192 records, 4 fields): 1 millis CompletedMACS2peakCalling