Job ID = 14157877 SRX = SRX10040008 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13723796 spots for SRR13642813/SRR13642813.sra Written 13723796 spots for SRR13642813/SRR13642813.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158072 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:03:09 13723796 reads; of these: 13723796 (100.00%) were unpaired; of these: 989762 (7.21%) aligned 0 times 10360792 (75.50%) aligned exactly 1 time 2373242 (17.29%) aligned >1 times 92.79% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 1151312 / 12734034 = 0.0904 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 @ Wed, 08 Dec 2021 12:15:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.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 @ Wed, 08 Dec 2021 12:15:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:15:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:15:26: 1000000 INFO @ Wed, 08 Dec 2021 12:15:31: 2000000 INFO @ Wed, 08 Dec 2021 12:15:36: 3000000 INFO @ Wed, 08 Dec 2021 12:15:41: 4000000 INFO @ Wed, 08 Dec 2021 12:15:46: 5000000 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 @ Wed, 08 Dec 2021 12:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.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 @ Wed, 08 Dec 2021 12:15:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:15:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:15:51: 6000000 INFO @ Wed, 08 Dec 2021 12:15:56: 1000000 INFO @ Wed, 08 Dec 2021 12:15:56: 7000000 INFO @ Wed, 08 Dec 2021 12:16:02: 8000000 INFO @ Wed, 08 Dec 2021 12:16:03: 2000000 INFO @ Wed, 08 Dec 2021 12:16:08: 9000000 INFO @ Wed, 08 Dec 2021 12:16:09: 3000000 INFO @ Wed, 08 Dec 2021 12:16:14: 10000000 INFO @ Wed, 08 Dec 2021 12:16:15: 4000000 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 @ Wed, 08 Dec 2021 12:16:19: 11000000 INFO @ Wed, 08 Dec 2021 12:16:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.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 @ Wed, 08 Dec 2021 12:16:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:16:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:16:21: 5000000 INFO @ Wed, 08 Dec 2021 12:16:22: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 12:16:22: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 12:16:22: #1 total tags in treatment: 11582722 INFO @ Wed, 08 Dec 2021 12:16:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:16:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:16:23: #1 tags after filtering in treatment: 11582722 INFO @ Wed, 08 Dec 2021 12:16:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:16:23: #1 finished! INFO @ Wed, 08 Dec 2021 12:16:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:16:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:16:23: #2 number of paired peaks: 280 WARNING @ Wed, 08 Dec 2021 12:16:23: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Wed, 08 Dec 2021 12:16:23: start model_add_line... INFO @ Wed, 08 Dec 2021 12:16:23: start X-correlation... INFO @ Wed, 08 Dec 2021 12:16:24: end of X-cor INFO @ Wed, 08 Dec 2021 12:16:24: #2 finished! INFO @ Wed, 08 Dec 2021 12:16:24: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 12:16:24: #2 alternative fragment length(s) may be 2,48,560 bps INFO @ Wed, 08 Dec 2021 12:16:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.05_model.r WARNING @ Wed, 08 Dec 2021 12:16:24: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:16:24: #2 You may need to consider one of the other alternative d(s): 2,48,560 WARNING @ Wed, 08 Dec 2021 12:16:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:16:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:16:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:16:26: 1000000 INFO @ Wed, 08 Dec 2021 12:16:28: 6000000 INFO @ Wed, 08 Dec 2021 12:16:33: 2000000 INFO @ Wed, 08 Dec 2021 12:16:34: 7000000 INFO @ Wed, 08 Dec 2021 12:16:39: 3000000 INFO @ Wed, 08 Dec 2021 12:16:40: 8000000 INFO @ Wed, 08 Dec 2021 12:16:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:16:45: 4000000 INFO @ Wed, 08 Dec 2021 12:16:46: 9000000 INFO @ Wed, 08 Dec 2021 12:16:51: 5000000 INFO @ Wed, 08 Dec 2021 12:16:52: 10000000 INFO @ Wed, 08 Dec 2021 12:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:16:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.05_summits.bed INFO @ Wed, 08 Dec 2021 12:16:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (616 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:16:58: 6000000 INFO @ Wed, 08 Dec 2021 12:16:59: 11000000 INFO @ Wed, 08 Dec 2021 12:17:02: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 12:17:02: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 12:17:02: #1 total tags in treatment: 11582722 INFO @ Wed, 08 Dec 2021 12:17:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:17:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:17:02: #1 tags after filtering in treatment: 11582722 INFO @ Wed, 08 Dec 2021 12:17:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:17:02: #1 finished! INFO @ Wed, 08 Dec 2021 12:17:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:17:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:17:03: #2 number of paired peaks: 280 WARNING @ Wed, 08 Dec 2021 12:17:03: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Wed, 08 Dec 2021 12:17:03: start model_add_line... INFO @ Wed, 08 Dec 2021 12:17:03: start X-correlation... INFO @ Wed, 08 Dec 2021 12:17:03: end of X-cor INFO @ Wed, 08 Dec 2021 12:17:03: #2 finished! INFO @ Wed, 08 Dec 2021 12:17:03: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 12:17:03: #2 alternative fragment length(s) may be 2,48,560 bps INFO @ Wed, 08 Dec 2021 12:17:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.10_model.r WARNING @ Wed, 08 Dec 2021 12:17:03: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:17:03: #2 You may need to consider one of the other alternative d(s): 2,48,560 WARNING @ Wed, 08 Dec 2021 12:17:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:17:03: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:17:04: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:17:10: 8000000 INFO @ Wed, 08 Dec 2021 12:17:16: 9000000 INFO @ Wed, 08 Dec 2021 12:17:22: 10000000 INFO @ Wed, 08 Dec 2021 12:17:23: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:17:28: 11000000 INFO @ Wed, 08 Dec 2021 12:17:32: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 12:17:32: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 12:17:32: #1 total tags in treatment: 11582722 INFO @ Wed, 08 Dec 2021 12:17:32: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:17:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:17:32: #1 tags after filtering in treatment: 11582722 INFO @ Wed, 08 Dec 2021 12:17:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:17:32: #1 finished! INFO @ Wed, 08 Dec 2021 12:17:32: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:17:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:17:32: #2 number of paired peaks: 280 WARNING @ Wed, 08 Dec 2021 12:17:32: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Wed, 08 Dec 2021 12:17:32: start model_add_line... INFO @ Wed, 08 Dec 2021 12:17:33: start X-correlation... INFO @ Wed, 08 Dec 2021 12:17:33: end of X-cor INFO @ Wed, 08 Dec 2021 12:17:33: #2 finished! INFO @ Wed, 08 Dec 2021 12:17:33: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 12:17:33: #2 alternative fragment length(s) may be 2,48,560 bps INFO @ Wed, 08 Dec 2021 12:17:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.20_model.r WARNING @ Wed, 08 Dec 2021 12:17:33: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:17:33: #2 You may need to consider one of the other alternative d(s): 2,48,560 WARNING @ Wed, 08 Dec 2021 12:17:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:17:33: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:17:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:17:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:17:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.10_summits.bed INFO @ Wed, 08 Dec 2021 12:17:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (360 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:17:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:18:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:18:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:18:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040008/SRX10040008.20_summits.bed INFO @ Wed, 08 Dec 2021 12:18:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (156 records, 4 fields): 2 millis CompletedMACS2peakCalling