Job ID = 10165658 SRX = SRX7879263 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34859115 spots for SRR11272878/SRR11272878.sra Written 34859115 spots for SRR11272878/SRR11272878.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165868 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:19 34859115 reads; of these: 34859115 (100.00%) were unpaired; of these: 17613808 (50.53%) aligned 0 times 14475259 (41.53%) aligned exactly 1 time 2770048 (7.95%) aligned >1 times 49.47% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 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] 12612245 / 17245307 = 0.7313 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 @ Thu, 08 Oct 2020 19:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.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 @ Thu, 08 Oct 2020 19:42:25: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:42:25: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:42:30: 1000000 INFO @ Thu, 08 Oct 2020 19:42:34: 2000000 INFO @ Thu, 08 Oct 2020 19:42:39: 3000000 INFO @ Thu, 08 Oct 2020 19:42:43: 4000000 INFO @ Thu, 08 Oct 2020 19:42:46: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:42:46: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:42:46: #1 total tags in treatment: 4633062 INFO @ Thu, 08 Oct 2020 19:42:46: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:42:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:42:46: #1 tags after filtering in treatment: 4633062 INFO @ Thu, 08 Oct 2020 19:42:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:42:46: #1 finished! INFO @ Thu, 08 Oct 2020 19:42:46: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:42:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:42:47: #2 number of paired peaks: 674 WARNING @ Thu, 08 Oct 2020 19:42:47: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Thu, 08 Oct 2020 19:42:47: start model_add_line... INFO @ Thu, 08 Oct 2020 19:42:47: start X-correlation... INFO @ Thu, 08 Oct 2020 19:42:47: end of X-cor INFO @ Thu, 08 Oct 2020 19:42:47: #2 finished! INFO @ Thu, 08 Oct 2020 19:42:47: #2 predicted fragment length is 49 bps INFO @ Thu, 08 Oct 2020 19:42:47: #2 alternative fragment length(s) may be 3,49 bps INFO @ Thu, 08 Oct 2020 19:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.05_model.r WARNING @ Thu, 08 Oct 2020 19:42:47: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:42:47: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Thu, 08 Oct 2020 19:42:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:42:47: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:42:47: #3 Pre-compute pvalue-qvalue table... 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 @ Thu, 08 Oct 2020 19:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.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 @ Thu, 08 Oct 2020 19:42:55: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:42:55: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:42:57: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:43:00: 1000000 INFO @ Thu, 08 Oct 2020 19:43:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:43:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:43:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.05_summits.bed INFO @ Thu, 08 Oct 2020 19:43:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (797 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:43:04: 2000000 INFO @ Thu, 08 Oct 2020 19:43:09: 3000000 INFO @ Thu, 08 Oct 2020 19:43:13: 4000000 INFO @ Thu, 08 Oct 2020 19:43:16: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:43:16: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:43:16: #1 total tags in treatment: 4633062 INFO @ Thu, 08 Oct 2020 19:43:16: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:43:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:43:16: #1 tags after filtering in treatment: 4633062 INFO @ Thu, 08 Oct 2020 19:43:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:43:16: #1 finished! INFO @ Thu, 08 Oct 2020 19:43:16: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:43:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:43:16: #2 number of paired peaks: 674 WARNING @ Thu, 08 Oct 2020 19:43:16: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Thu, 08 Oct 2020 19:43:16: start model_add_line... INFO @ Thu, 08 Oct 2020 19:43:17: start X-correlation... INFO @ Thu, 08 Oct 2020 19:43:17: end of X-cor INFO @ Thu, 08 Oct 2020 19:43:17: #2 finished! INFO @ Thu, 08 Oct 2020 19:43:17: #2 predicted fragment length is 49 bps INFO @ Thu, 08 Oct 2020 19:43:17: #2 alternative fragment length(s) may be 3,49 bps INFO @ Thu, 08 Oct 2020 19:43:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.10_model.r WARNING @ Thu, 08 Oct 2020 19:43:17: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:43:17: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Thu, 08 Oct 2020 19:43:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:43:17: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:43:17: #3 Pre-compute pvalue-qvalue table... 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 @ Thu, 08 Oct 2020 19:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.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 @ Thu, 08 Oct 2020 19:43:25: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:43:25: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:43:26: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:43:30: 1000000 INFO @ Thu, 08 Oct 2020 19:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.10_summits.bed INFO @ Thu, 08 Oct 2020 19:43:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (577 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:43:34: 2000000 INFO @ Thu, 08 Oct 2020 19:43:39: 3000000 INFO @ Thu, 08 Oct 2020 19:43:43: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:43:46: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:43:46: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:43:46: #1 total tags in treatment: 4633062 INFO @ Thu, 08 Oct 2020 19:43:46: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:43:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:43:46: #1 tags after filtering in treatment: 4633062 INFO @ Thu, 08 Oct 2020 19:43:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:43:46: #1 finished! INFO @ Thu, 08 Oct 2020 19:43:46: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:43:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:43:47: #2 number of paired peaks: 674 WARNING @ Thu, 08 Oct 2020 19:43:47: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Thu, 08 Oct 2020 19:43:47: start model_add_line... INFO @ Thu, 08 Oct 2020 19:43:47: start X-correlation... INFO @ Thu, 08 Oct 2020 19:43:47: end of X-cor INFO @ Thu, 08 Oct 2020 19:43:47: #2 finished! INFO @ Thu, 08 Oct 2020 19:43:47: #2 predicted fragment length is 49 bps INFO @ Thu, 08 Oct 2020 19:43:47: #2 alternative fragment length(s) may be 3,49 bps INFO @ Thu, 08 Oct 2020 19:43:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.20_model.r WARNING @ Thu, 08 Oct 2020 19:43:47: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:43:47: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Thu, 08 Oct 2020 19:43:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:43:47: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:43:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:43:57: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:44:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:44:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:44:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879263/SRX7879263.20_summits.bed INFO @ Thu, 08 Oct 2020 19:44:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (233 records, 4 fields): 1 millis CompletedMACS2peakCalling