Job ID = 16434951 SRX = SRX10435532 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13590622 spots for SRR14060932/SRR14060932.sra Written 13590622 spots for SRR14060932/SRR14060932.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435005 ("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: 00:04:00 13590622 reads; of these: 13590622 (100.00%) were unpaired; of these: 2294923 (16.89%) aligned 0 times 9471464 (69.69%) aligned exactly 1 time 1824235 (13.42%) aligned >1 times 83.11% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 1756194 / 11295699 = 0.1555 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:27:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.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 @ Tue, 02 Aug 2022 10:27:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:27:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:27:12: 1000000 INFO @ Tue, 02 Aug 2022 10:27:17: 2000000 INFO @ Tue, 02 Aug 2022 10:27:21: 3000000 INFO @ Tue, 02 Aug 2022 10:27:26: 4000000 INFO @ Tue, 02 Aug 2022 10:27:31: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:27:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.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 @ Tue, 02 Aug 2022 10:27:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:27:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:27:36: 6000000 INFO @ Tue, 02 Aug 2022 10:27:41: 1000000 INFO @ Tue, 02 Aug 2022 10:27:41: 7000000 INFO @ Tue, 02 Aug 2022 10:27:46: 8000000 INFO @ Tue, 02 Aug 2022 10:27:46: 2000000 INFO @ Tue, 02 Aug 2022 10:27:51: 9000000 INFO @ Tue, 02 Aug 2022 10:27:51: 3000000 INFO @ Tue, 02 Aug 2022 10:27:53: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:27:53: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:27:53: #1 total tags in treatment: 9539505 INFO @ Tue, 02 Aug 2022 10:27:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:27:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:27:54: #1 tags after filtering in treatment: 9539505 INFO @ Tue, 02 Aug 2022 10:27:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:27:54: #1 finished! INFO @ Tue, 02 Aug 2022 10:27:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:27:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:27:54: #2 number of paired peaks: 631 WARNING @ Tue, 02 Aug 2022 10:27:54: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Tue, 02 Aug 2022 10:27:54: start model_add_line... INFO @ Tue, 02 Aug 2022 10:27:54: start X-correlation... INFO @ Tue, 02 Aug 2022 10:27:54: end of X-cor INFO @ Tue, 02 Aug 2022 10:27:54: #2 finished! INFO @ Tue, 02 Aug 2022 10:27:54: #2 predicted fragment length is 124 bps INFO @ Tue, 02 Aug 2022 10:27:54: #2 alternative fragment length(s) may be 124 bps INFO @ Tue, 02 Aug 2022 10:27:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.05_model.r WARNING @ Tue, 02 Aug 2022 10:27:54: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:27:54: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Tue, 02 Aug 2022 10:27:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:27:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:27:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:27:56: 4000000 INFO @ Tue, 02 Aug 2022 10:28:01: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:28:06: 6000000 INFO @ Tue, 02 Aug 2022 10:28:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.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 @ Tue, 02 Aug 2022 10:28:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:28:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:28:11: 7000000 INFO @ Tue, 02 Aug 2022 10:28:11: 1000000 INFO @ Tue, 02 Aug 2022 10:28:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:28:16: 8000000 INFO @ Tue, 02 Aug 2022 10:28:17: 2000000 INFO @ Tue, 02 Aug 2022 10:28:21: 9000000 INFO @ Tue, 02 Aug 2022 10:28:22: 3000000 INFO @ Tue, 02 Aug 2022 10:28:24: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:28:24: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:28:24: #1 total tags in treatment: 9539505 INFO @ Tue, 02 Aug 2022 10:28:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:28:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:28:24: #1 tags after filtering in treatment: 9539505 INFO @ Tue, 02 Aug 2022 10:28:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:28:24: #1 finished! INFO @ Tue, 02 Aug 2022 10:28:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:28:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:28:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:28:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:28:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.05_summits.bed INFO @ Tue, 02 Aug 2022 10:28:24: Done! INFO @ Tue, 02 Aug 2022 10:28:24: #2 number of paired peaks: 631 WARNING @ Tue, 02 Aug 2022 10:28:24: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Tue, 02 Aug 2022 10:28:24: start model_add_line... INFO @ Tue, 02 Aug 2022 10:28:24: start X-correlation... INFO @ Tue, 02 Aug 2022 10:28:24: end of X-cor INFO @ Tue, 02 Aug 2022 10:28:24: #2 finished! INFO @ Tue, 02 Aug 2022 10:28:24: #2 predicted fragment length is 124 bps INFO @ Tue, 02 Aug 2022 10:28:24: #2 alternative fragment length(s) may be 124 bps INFO @ Tue, 02 Aug 2022 10:28:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.10_model.r WARNING @ Tue, 02 Aug 2022 10:28:25: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:28:25: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Tue, 02 Aug 2022 10:28:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:28:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:28:25: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1714 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:28:27: 4000000 INFO @ Tue, 02 Aug 2022 10:28:32: 5000000 INFO @ Tue, 02 Aug 2022 10:28:37: 6000000 INFO @ Tue, 02 Aug 2022 10:28:42: 7000000 INFO @ Tue, 02 Aug 2022 10:28:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:28:47: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:28:52: 9000000 INFO @ Tue, 02 Aug 2022 10:28:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:28:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:28:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.10_summits.bed INFO @ Tue, 02 Aug 2022 10:28:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1117 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:28:55: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:28:55: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:28:55: #1 total tags in treatment: 9539505 INFO @ Tue, 02 Aug 2022 10:28:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:28:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:28:55: #1 tags after filtering in treatment: 9539505 INFO @ Tue, 02 Aug 2022 10:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:28:55: #1 finished! INFO @ Tue, 02 Aug 2022 10:28:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:28:55: #2 number of paired peaks: 631 WARNING @ Tue, 02 Aug 2022 10:28:55: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Tue, 02 Aug 2022 10:28:55: start model_add_line... INFO @ Tue, 02 Aug 2022 10:28:55: start X-correlation... INFO @ Tue, 02 Aug 2022 10:28:55: end of X-cor INFO @ Tue, 02 Aug 2022 10:28:55: #2 finished! INFO @ Tue, 02 Aug 2022 10:28:55: #2 predicted fragment length is 124 bps INFO @ Tue, 02 Aug 2022 10:28:55: #2 alternative fragment length(s) may be 124 bps INFO @ Tue, 02 Aug 2022 10:28:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.20_model.r WARNING @ Tue, 02 Aug 2022 10:28:55: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:28:55: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Tue, 02 Aug 2022 10:28:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:28:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:28:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:29:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:29:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:29:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:29:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435532/SRX10435532.20_summits.bed INFO @ Tue, 02 Aug 2022 10:29:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (679 records, 4 fields): 18 millis CompletedMACS2peakCalling