Job ID = 14160616 SRX = SRX10399031 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13764712 spots for SRR14022419/SRR14022419.sra Written 13764712 spots for SRR14022419/SRR14022419.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160749 ("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: 00:04:20 13764712 reads; of these: 13764712 (100.00%) were unpaired; of these: 501239 (3.64%) aligned 0 times 11092121 (80.58%) aligned exactly 1 time 2171352 (15.77%) aligned >1 times 96.36% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 1219750 / 13263473 = 0.0920 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:35:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.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, 09 Dec 2021 03:35:23: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:35:23: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:35:30: 1000000 INFO @ Thu, 09 Dec 2021 03:35:37: 2000000 INFO @ Thu, 09 Dec 2021 03:35:44: 3000000 INFO @ Thu, 09 Dec 2021 03:35:50: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:35:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.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, 09 Dec 2021 03:35:55: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:35:55: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:35:57: 5000000 INFO @ Thu, 09 Dec 2021 03:36:03: 1000000 INFO @ Thu, 09 Dec 2021 03:36:03: 6000000 INFO @ Thu, 09 Dec 2021 03:36:09: 7000000 INFO @ Thu, 09 Dec 2021 03:36:12: 2000000 INFO @ Thu, 09 Dec 2021 03:36:16: 8000000 INFO @ Thu, 09 Dec 2021 03:36:19: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:36:23: 9000000 INFO @ Thu, 09 Dec 2021 03:36:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.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, 09 Dec 2021 03:36:24: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:36:24: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:36:26: 4000000 INFO @ Thu, 09 Dec 2021 03:36:31: 10000000 INFO @ Thu, 09 Dec 2021 03:36:32: 1000000 INFO @ Thu, 09 Dec 2021 03:36:33: 5000000 INFO @ Thu, 09 Dec 2021 03:36:39: 6000000 INFO @ Thu, 09 Dec 2021 03:36:39: 2000000 INFO @ Thu, 09 Dec 2021 03:36:39: 11000000 INFO @ Thu, 09 Dec 2021 03:36:45: 7000000 INFO @ Thu, 09 Dec 2021 03:36:46: 3000000 INFO @ Thu, 09 Dec 2021 03:36:47: 12000000 INFO @ Thu, 09 Dec 2021 03:36:47: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:36:47: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:36:47: #1 total tags in treatment: 12043723 INFO @ Thu, 09 Dec 2021 03:36:47: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:36:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:36:47: #1 tags after filtering in treatment: 12043723 INFO @ Thu, 09 Dec 2021 03:36:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:36:47: #1 finished! INFO @ Thu, 09 Dec 2021 03:36:47: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:36:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:36:48: #2 number of paired peaks: 269 WARNING @ Thu, 09 Dec 2021 03:36:48: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Thu, 09 Dec 2021 03:36:48: start model_add_line... INFO @ Thu, 09 Dec 2021 03:36:48: start X-correlation... INFO @ Thu, 09 Dec 2021 03:36:48: end of X-cor INFO @ Thu, 09 Dec 2021 03:36:48: #2 finished! INFO @ Thu, 09 Dec 2021 03:36:48: #2 predicted fragment length is 75 bps INFO @ Thu, 09 Dec 2021 03:36:48: #2 alternative fragment length(s) may be 4,75 bps INFO @ Thu, 09 Dec 2021 03:36:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.05_model.r WARNING @ Thu, 09 Dec 2021 03:36:48: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:36:48: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Thu, 09 Dec 2021 03:36:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:36:48: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:36:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:36:51: 8000000 INFO @ Thu, 09 Dec 2021 03:36:53: 4000000 INFO @ Thu, 09 Dec 2021 03:36:58: 9000000 INFO @ Thu, 09 Dec 2021 03:37:01: 5000000 INFO @ Thu, 09 Dec 2021 03:37:05: 10000000 INFO @ Thu, 09 Dec 2021 03:37:07: 6000000 INFO @ Thu, 09 Dec 2021 03:37:12: 11000000 INFO @ Thu, 09 Dec 2021 03:37:13: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:37:14: 7000000 INFO @ Thu, 09 Dec 2021 03:37:20: 12000000 INFO @ Thu, 09 Dec 2021 03:37:20: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:37:20: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:37:20: #1 total tags in treatment: 12043723 INFO @ Thu, 09 Dec 2021 03:37:20: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:37:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:37:21: #1 tags after filtering in treatment: 12043723 INFO @ Thu, 09 Dec 2021 03:37:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:37:21: #1 finished! INFO @ Thu, 09 Dec 2021 03:37:21: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:37:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:37:21: 8000000 INFO @ Thu, 09 Dec 2021 03:37:21: #2 number of paired peaks: 269 WARNING @ Thu, 09 Dec 2021 03:37:21: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Thu, 09 Dec 2021 03:37:21: start model_add_line... INFO @ Thu, 09 Dec 2021 03:37:22: start X-correlation... INFO @ Thu, 09 Dec 2021 03:37:22: end of X-cor INFO @ Thu, 09 Dec 2021 03:37:22: #2 finished! INFO @ Thu, 09 Dec 2021 03:37:22: #2 predicted fragment length is 75 bps INFO @ Thu, 09 Dec 2021 03:37:22: #2 alternative fragment length(s) may be 4,75 bps INFO @ Thu, 09 Dec 2021 03:37:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.10_model.r WARNING @ Thu, 09 Dec 2021 03:37:22: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:37:22: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Thu, 09 Dec 2021 03:37:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:37:22: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:37:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:37:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:37:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:37:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.05_summits.bed INFO @ Thu, 09 Dec 2021 03:37:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (575 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:37:29: 9000000 INFO @ Thu, 09 Dec 2021 03:37:37: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:37:44: 11000000 INFO @ Thu, 09 Dec 2021 03:37:51: 12000000 INFO @ Thu, 09 Dec 2021 03:37:52: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:37:52: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:37:52: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:37:52: #1 total tags in treatment: 12043723 INFO @ Thu, 09 Dec 2021 03:37:52: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:37:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:37:52: #1 tags after filtering in treatment: 12043723 INFO @ Thu, 09 Dec 2021 03:37:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:37:52: #1 finished! INFO @ Thu, 09 Dec 2021 03:37:52: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:37:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:37:53: #2 number of paired peaks: 269 WARNING @ Thu, 09 Dec 2021 03:37:53: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Thu, 09 Dec 2021 03:37:53: start model_add_line... INFO @ Thu, 09 Dec 2021 03:37:53: start X-correlation... INFO @ Thu, 09 Dec 2021 03:37:53: end of X-cor INFO @ Thu, 09 Dec 2021 03:37:53: #2 finished! INFO @ Thu, 09 Dec 2021 03:37:53: #2 predicted fragment length is 75 bps INFO @ Thu, 09 Dec 2021 03:37:53: #2 alternative fragment length(s) may be 4,75 bps INFO @ Thu, 09 Dec 2021 03:37:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.20_model.r WARNING @ Thu, 09 Dec 2021 03:37:53: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:37:53: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Thu, 09 Dec 2021 03:37:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:37:53: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:37:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:38:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:38:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:38:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.10_summits.bed INFO @ Thu, 09 Dec 2021 03:38:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:38:19: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:38:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:38:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:38:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399031/SRX10399031.20_summits.bed INFO @ Thu, 09 Dec 2021 03:38:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 2 millis CompletedMACS2peakCalling