Job ID = 12264801 SRX = SRX7246258 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8890308 spots for SRR10564649/SRR10564649.sra Written 8890308 spots for SRR10564649/SRR10564649.sra Read 9279248 spots for SRR10564650/SRR10564650.sra Written 9279248 spots for SRR10564650/SRR10564650.sra Read 1857951 spots for SRR10564651/SRR10564651.sra Written 1857951 spots for SRR10564651/SRR10564651.sra Read 1857951 spots for SRR10564652/SRR10564652.sra Written 1857951 spots for SRR10564652/SRR10564652.sra Read 1865837 spots for SRR10564653/SRR10564653.sra Written 1865837 spots for SRR10564653/SRR10564653.sra Read 1865837 spots for SRR10564654/SRR10564654.sra Written 1865837 spots for SRR10564654/SRR10564654.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265067 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:33 25617132 reads; of these: 25617132 (100.00%) were unpaired; of these: 920251 (3.59%) aligned 0 times 21651599 (84.52%) aligned exactly 1 time 3045282 (11.89%) aligned >1 times 96.41% overall alignment rate Time searching: 00:05:33 Overall time: 00:05:33 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 12 files... [bam_rmdupse_core] 12695168 / 24696881 = 0.5140 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 06:06:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.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 06:06:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:06:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:06:31: 1000000 INFO @ Sat, 03 Apr 2021 06:06:37: 2000000 INFO @ Sat, 03 Apr 2021 06:06:42: 3000000 INFO @ Sat, 03 Apr 2021 06:06:48: 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 06:06:53: 5000000 INFO @ Sat, 03 Apr 2021 06:06:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.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 06:06:54: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:06:54: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:06:59: 6000000 INFO @ Sat, 03 Apr 2021 06:07:03: 1000000 INFO @ Sat, 03 Apr 2021 06:07:05: 7000000 INFO @ Sat, 03 Apr 2021 06:07:11: 8000000 INFO @ Sat, 03 Apr 2021 06:07:11: 2000000 INFO @ Sat, 03 Apr 2021 06:07:17: 9000000 INFO @ Sat, 03 Apr 2021 06:07:19: 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 06:07:23: 10000000 INFO @ Sat, 03 Apr 2021 06:07:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.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 06:07:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:07:24: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:07:28: 4000000 INFO @ Sat, 03 Apr 2021 06:07:29: 11000000 INFO @ Sat, 03 Apr 2021 06:07:31: 1000000 INFO @ Sat, 03 Apr 2021 06:07:35: 12000000 INFO @ Sat, 03 Apr 2021 06:07:35: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:07:35: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:07:35: #1 total tags in treatment: 12001713 INFO @ Sat, 03 Apr 2021 06:07:35: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:07:35: #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 06:07:35: #1 tags after filtering in treatment: 12001713 INFO @ Sat, 03 Apr 2021 06:07:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:07:35: #1 finished! INFO @ Sat, 03 Apr 2021 06:07:35: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:07:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:07:36: #2 number of paired peaks: 610 WARNING @ Sat, 03 Apr 2021 06:07:36: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Sat, 03 Apr 2021 06:07:36: start model_add_line... INFO @ Sat, 03 Apr 2021 06:07:36: start X-correlation... INFO @ Sat, 03 Apr 2021 06:07:36: end of X-cor INFO @ Sat, 03 Apr 2021 06:07:36: #2 finished! INFO @ Sat, 03 Apr 2021 06:07:36: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Apr 2021 06:07:36: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 03 Apr 2021 06:07:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.05_model.r WARNING @ Sat, 03 Apr 2021 06:07:36: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:07:36: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 03 Apr 2021 06:07:36: #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 06:07:36: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:07:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:07:37: 5000000 INFO @ Sat, 03 Apr 2021 06:07:37: 2000000 INFO @ Sat, 03 Apr 2021 06:07:42: 3000000 INFO @ Sat, 03 Apr 2021 06:07:46: 6000000 INFO @ Sat, 03 Apr 2021 06:07:47: 4000000 INFO @ Sat, 03 Apr 2021 06:07:53: 5000000 INFO @ Sat, 03 Apr 2021 06:07:54: 7000000 INFO @ Sat, 03 Apr 2021 06:07:58: 6000000 INFO @ Sat, 03 Apr 2021 06:08:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:08:02: 8000000 INFO @ Sat, 03 Apr 2021 06:08:05: 7000000 INFO @ Sat, 03 Apr 2021 06:08:11: 8000000 INFO @ Sat, 03 Apr 2021 06:08:11: 9000000 INFO @ Sat, 03 Apr 2021 06:08:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:08:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:08:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.05_summits.bed INFO @ Sat, 03 Apr 2021 06:08:13: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8209 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:08:16: 9000000 INFO @ Sat, 03 Apr 2021 06:08:20: 10000000 INFO @ Sat, 03 Apr 2021 06:08:22: 10000000 INFO @ Sat, 03 Apr 2021 06:08:28: 11000000 INFO @ Sat, 03 Apr 2021 06:08:29: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:08:33: 12000000 INFO @ Sat, 03 Apr 2021 06:08:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:08:33: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:08:33: #1 total tags in treatment: 12001713 INFO @ Sat, 03 Apr 2021 06:08:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:08:33: #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 06:08:33: #1 tags after filtering in treatment: 12001713 INFO @ Sat, 03 Apr 2021 06:08:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:08:33: #1 finished! INFO @ Sat, 03 Apr 2021 06:08:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:08:34: #2 number of paired peaks: 610 WARNING @ Sat, 03 Apr 2021 06:08:34: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Sat, 03 Apr 2021 06:08:34: start model_add_line... INFO @ Sat, 03 Apr 2021 06:08:34: start X-correlation... INFO @ Sat, 03 Apr 2021 06:08:34: end of X-cor INFO @ Sat, 03 Apr 2021 06:08:34: #2 finished! INFO @ Sat, 03 Apr 2021 06:08:34: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Apr 2021 06:08:34: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 03 Apr 2021 06:08:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.20_model.r WARNING @ Sat, 03 Apr 2021 06:08:34: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:08:34: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 03 Apr 2021 06:08:34: #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 06:08:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:08:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:08:37: 12000000 INFO @ Sat, 03 Apr 2021 06:08:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:08:37: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:08:37: #1 total tags in treatment: 12001713 INFO @ Sat, 03 Apr 2021 06:08:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:08:37: #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 06:08:37: #1 tags after filtering in treatment: 12001713 INFO @ Sat, 03 Apr 2021 06:08:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:08:37: #1 finished! INFO @ Sat, 03 Apr 2021 06:08:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:08:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:08:38: #2 number of paired peaks: 610 WARNING @ Sat, 03 Apr 2021 06:08:38: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Sat, 03 Apr 2021 06:08:38: start model_add_line... INFO @ Sat, 03 Apr 2021 06:08:38: start X-correlation... INFO @ Sat, 03 Apr 2021 06:08:39: end of X-cor INFO @ Sat, 03 Apr 2021 06:08:39: #2 finished! INFO @ Sat, 03 Apr 2021 06:08:39: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Apr 2021 06:08:39: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 03 Apr 2021 06:08:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.10_model.r WARNING @ Sat, 03 Apr 2021 06:08:39: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:08:39: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 03 Apr 2021 06:08:39: #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 06:08:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:08:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:08:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:09:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:09:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:09:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:09:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.20_summits.bed INFO @ Sat, 03 Apr 2021 06:09:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2320 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:09:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:09:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:09:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246258/SRX7246258.10_summits.bed INFO @ Sat, 03 Apr 2021 06:09:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5223 records, 4 fields): 8 millis CompletedMACS2peakCalling