Job ID = 12264806 SRX = SRX7246263 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8294249 spots for SRR10564669/SRR10564669.sra Written 8294249 spots for SRR10564669/SRR10564669.sra Read 8532239 spots for SRR10564670/SRR10564670.sra Written 8532239 spots for SRR10564670/SRR10564670.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265020 ("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: 00:03:06 16826488 reads; of these: 16826488 (100.00%) were unpaired; of these: 4146101 (24.64%) aligned 0 times 10793889 (64.15%) aligned exactly 1 time 1886498 (11.21%) aligned >1 times 75.36% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 4904071 / 12680387 = 0.3867 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.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 @ Sat, 03 Apr 2021 06:01:03: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:01:03: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:01:10: 1000000 INFO @ Sat, 03 Apr 2021 06:01:18: 2000000 INFO @ Sat, 03 Apr 2021 06:01:26: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:01:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.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 @ Sat, 03 Apr 2021 06:01:33: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:01:33: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:01:34: 4000000 INFO @ Sat, 03 Apr 2021 06:01:41: 1000000 INFO @ Sat, 03 Apr 2021 06:01:41: 5000000 INFO @ Sat, 03 Apr 2021 06:01:49: 6000000 INFO @ Sat, 03 Apr 2021 06:01:49: 2000000 INFO @ Sat, 03 Apr 2021 06:01:57: 7000000 INFO @ Sat, 03 Apr 2021 06:01:57: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:02:02: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:02:02: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:02:02: #1 total tags in treatment: 7776316 INFO @ Sat, 03 Apr 2021 06:02:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:02:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:02:02: #1 tags after filtering in treatment: 7776316 INFO @ Sat, 03 Apr 2021 06:02:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:02:02: #1 finished! INFO @ Sat, 03 Apr 2021 06:02:02: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:02:03: #2 number of paired peaks: 715 WARNING @ Sat, 03 Apr 2021 06:02:03: Fewer paired peaks (715) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 715 pairs to build model! INFO @ Sat, 03 Apr 2021 06:02:03: start model_add_line... INFO @ Sat, 03 Apr 2021 06:02:03: start X-correlation... INFO @ Sat, 03 Apr 2021 06:02:03: end of X-cor INFO @ Sat, 03 Apr 2021 06:02:03: #2 finished! INFO @ Sat, 03 Apr 2021 06:02:03: #2 predicted fragment length is 93 bps INFO @ Sat, 03 Apr 2021 06:02:03: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 03 Apr 2021 06:02:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.05_model.r WARNING @ Sat, 03 Apr 2021 06:02:03: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:02:03: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 03 Apr 2021 06:02:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:02:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:02:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:02:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.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 @ Sat, 03 Apr 2021 06:02:03: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:03: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:04: 4000000 INFO @ Sat, 03 Apr 2021 06:02:10: 1000000 INFO @ Sat, 03 Apr 2021 06:02:12: 5000000 INFO @ Sat, 03 Apr 2021 06:02:16: 2000000 INFO @ Sat, 03 Apr 2021 06:02:19: 6000000 INFO @ Sat, 03 Apr 2021 06:02:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:02:22: 3000000 INFO @ Sat, 03 Apr 2021 06:02:25: 7000000 INFO @ Sat, 03 Apr 2021 06:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:02:27: 4000000 INFO @ Sat, 03 Apr 2021 06:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.05_summits.bed INFO @ Sat, 03 Apr 2021 06:02:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6144 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:02:30: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:02:30: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:02:30: #1 total tags in treatment: 7776316 INFO @ Sat, 03 Apr 2021 06:02:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:02:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:02:30: #1 tags after filtering in treatment: 7776316 INFO @ Sat, 03 Apr 2021 06:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:02:30: #1 finished! INFO @ Sat, 03 Apr 2021 06:02:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:02:31: #2 number of paired peaks: 715 WARNING @ Sat, 03 Apr 2021 06:02:31: Fewer paired peaks (715) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 715 pairs to build model! INFO @ Sat, 03 Apr 2021 06:02:31: start model_add_line... INFO @ Sat, 03 Apr 2021 06:02:31: start X-correlation... INFO @ Sat, 03 Apr 2021 06:02:31: end of X-cor INFO @ Sat, 03 Apr 2021 06:02:31: #2 finished! INFO @ Sat, 03 Apr 2021 06:02:31: #2 predicted fragment length is 93 bps INFO @ Sat, 03 Apr 2021 06:02:31: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 03 Apr 2021 06:02:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.10_model.r WARNING @ Sat, 03 Apr 2021 06:02:31: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:02:31: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 03 Apr 2021 06:02:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:02:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:02:33: 5000000 INFO @ Sat, 03 Apr 2021 06:02:39: 6000000 INFO @ Sat, 03 Apr 2021 06:02:44: 7000000 INFO @ Sat, 03 Apr 2021 06:02:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:02:49: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:02:49: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:02:49: #1 total tags in treatment: 7776316 INFO @ Sat, 03 Apr 2021 06:02:49: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:02:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:02:49: #1 tags after filtering in treatment: 7776316 INFO @ Sat, 03 Apr 2021 06:02:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:02:49: #1 finished! INFO @ Sat, 03 Apr 2021 06:02:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:02:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:02:50: #2 number of paired peaks: 715 WARNING @ Sat, 03 Apr 2021 06:02:50: Fewer paired peaks (715) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 715 pairs to build model! INFO @ Sat, 03 Apr 2021 06:02:50: start model_add_line... INFO @ Sat, 03 Apr 2021 06:02:50: start X-correlation... INFO @ Sat, 03 Apr 2021 06:02:50: end of X-cor INFO @ Sat, 03 Apr 2021 06:02:50: #2 finished! INFO @ Sat, 03 Apr 2021 06:02:50: #2 predicted fragment length is 93 bps INFO @ Sat, 03 Apr 2021 06:02:50: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 03 Apr 2021 06:02:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.20_model.r WARNING @ Sat, 03 Apr 2021 06:02:50: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:02:50: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 03 Apr 2021 06:02:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:02:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:02:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:02:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:02:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:02:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.10_summits.bed INFO @ Sat, 03 Apr 2021 06:02:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3636 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:03:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:03:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:03:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:03:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246263/SRX7246263.20_summits.bed INFO @ Sat, 03 Apr 2021 06:03:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1542 records, 4 fields): 14 millis CompletedMACS2peakCalling