Job ID = 12264752 SRX = SRX2969570 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34279594 spots for SRR5772133/SRR5772133.sra Written 34279594 spots for SRR5772133/SRR5772133.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265076 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:58 34279594 reads; of these: 34279594 (100.00%) were unpaired; of these: 2226727 (6.50%) aligned 0 times 29122163 (84.95%) aligned exactly 1 time 2930704 (8.55%) aligned >1 times 93.50% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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 16 files... [bam_rmdupse_core] 24397157 / 32052867 = 0.7612 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 06:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.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 06:07:40: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:07:40: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:07:47: 1000000 INFO @ Sat, 03 Apr 2021 06:07:53: 2000000 INFO @ Sat, 03 Apr 2021 06:07:59: 3000000 INFO @ Sat, 03 Apr 2021 06:08:05: 4000000 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 06:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.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 06:08:09: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:08:09: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:08:12: 5000000 INFO @ Sat, 03 Apr 2021 06:08:16: 1000000 INFO @ Sat, 03 Apr 2021 06:08:19: 6000000 INFO @ Sat, 03 Apr 2021 06:08:23: 2000000 INFO @ Sat, 03 Apr 2021 06:08:25: 7000000 INFO @ Sat, 03 Apr 2021 06:08:30: 3000000 INFO @ Sat, 03 Apr 2021 06:08:30: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:08:30: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:08:30: #1 total tags in treatment: 7655710 INFO @ Sat, 03 Apr 2021 06:08:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:08:30: #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 06:08:30: #1 tags after filtering in treatment: 7655710 INFO @ Sat, 03 Apr 2021 06:08:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:08:30: #1 finished! INFO @ Sat, 03 Apr 2021 06:08:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:08:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:08:30: #2 number of paired peaks: 668 WARNING @ Sat, 03 Apr 2021 06:08:30: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Sat, 03 Apr 2021 06:08:30: start model_add_line... INFO @ Sat, 03 Apr 2021 06:08:31: start X-correlation... INFO @ Sat, 03 Apr 2021 06:08:31: end of X-cor INFO @ Sat, 03 Apr 2021 06:08:31: #2 finished! INFO @ Sat, 03 Apr 2021 06:08:31: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Apr 2021 06:08:31: #2 alternative fragment length(s) may be 62 bps INFO @ Sat, 03 Apr 2021 06:08:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.05_model.r WARNING @ Sat, 03 Apr 2021 06:08:31: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:08:31: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sat, 03 Apr 2021 06:08:31: #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 06:08:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:08:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:08:36: 4000000 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 06:08:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.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 06:08:39: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:08:39: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:08:43: 5000000 INFO @ Sat, 03 Apr 2021 06:08:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:08:46: 1000000 INFO @ Sat, 03 Apr 2021 06:08:50: 6000000 INFO @ Sat, 03 Apr 2021 06:08:53: 2000000 INFO @ Sat, 03 Apr 2021 06:08:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:08:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:08:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.05_summits.bed INFO @ Sat, 03 Apr 2021 06:08:55: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6383 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:08:57: 7000000 INFO @ Sat, 03 Apr 2021 06:09:00: 3000000 INFO @ Sat, 03 Apr 2021 06:09:01: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:09:01: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:09:01: #1 total tags in treatment: 7655710 INFO @ Sat, 03 Apr 2021 06:09:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:09:01: #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 06:09:01: #1 tags after filtering in treatment: 7655710 INFO @ Sat, 03 Apr 2021 06:09:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:09:01: #1 finished! INFO @ Sat, 03 Apr 2021 06:09:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:09:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:09:02: #2 number of paired peaks: 668 WARNING @ Sat, 03 Apr 2021 06:09:02: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Sat, 03 Apr 2021 06:09:02: start model_add_line... INFO @ Sat, 03 Apr 2021 06:09:02: start X-correlation... INFO @ Sat, 03 Apr 2021 06:09:02: end of X-cor INFO @ Sat, 03 Apr 2021 06:09:02: #2 finished! INFO @ Sat, 03 Apr 2021 06:09:02: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Apr 2021 06:09:02: #2 alternative fragment length(s) may be 62 bps INFO @ Sat, 03 Apr 2021 06:09:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.10_model.r WARNING @ Sat, 03 Apr 2021 06:09:02: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:09:02: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sat, 03 Apr 2021 06:09:02: #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 06:09:02: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:09:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:09:07: 4000000 INFO @ Sat, 03 Apr 2021 06:09:13: 5000000 INFO @ Sat, 03 Apr 2021 06:09:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:09:20: 6000000 INFO @ Sat, 03 Apr 2021 06:09:26: 7000000 INFO @ Sat, 03 Apr 2021 06:09:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:09:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:09:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.10_summits.bed INFO @ Sat, 03 Apr 2021 06:09:27: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3403 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:09:30: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:09:30: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:09:30: #1 total tags in treatment: 7655710 INFO @ Sat, 03 Apr 2021 06:09:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:09:30: #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 06:09:30: #1 tags after filtering in treatment: 7655710 INFO @ Sat, 03 Apr 2021 06:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:09:30: #1 finished! INFO @ Sat, 03 Apr 2021 06:09:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:09:31: #2 number of paired peaks: 668 WARNING @ Sat, 03 Apr 2021 06:09:31: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Sat, 03 Apr 2021 06:09:31: start model_add_line... INFO @ Sat, 03 Apr 2021 06:09:31: start X-correlation... INFO @ Sat, 03 Apr 2021 06:09:31: end of X-cor INFO @ Sat, 03 Apr 2021 06:09:31: #2 finished! INFO @ Sat, 03 Apr 2021 06:09:31: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Apr 2021 06:09:31: #2 alternative fragment length(s) may be 62 bps INFO @ Sat, 03 Apr 2021 06:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.20_model.r WARNING @ Sat, 03 Apr 2021 06:09:31: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:09:31: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sat, 03 Apr 2021 06:09:31: #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 06:09:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:09:31: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:09:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:09:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:09:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:09:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2969570/SRX2969570.20_summits.bed INFO @ Sat, 03 Apr 2021 06:09:55: Done! pass1 - making usageList (6 chroms): 17 millis pass2 - checking and writing primary data (1122 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。