Job ID = 14159618 SRX = SRX3180783 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 10288657 spots for SRR6030434/SRR6030434.sra Written 10288657 spots for SRR6030434/SRR6030434.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160121 ("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: 00:01:58 10288657 reads; of these: 10288657 (100.00%) were unpaired; of these: 960387 (9.33%) aligned 0 times 7676437 (74.61%) aligned exactly 1 time 1651833 (16.05%) aligned >1 times 90.67% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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_rmdupse_core] 1079616 / 9328270 = 0.1157 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 23:32:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.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 23:32:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:32:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:32:44: 1000000 INFO @ Wed, 08 Dec 2021 23:32:49: 2000000 INFO @ Wed, 08 Dec 2021 23:32:53: 3000000 INFO @ Wed, 08 Dec 2021 23:32:58: 4000000 INFO @ Wed, 08 Dec 2021 23:33:02: 5000000 INFO @ Wed, 08 Dec 2021 23:33:07: 6000000 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 23:33:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.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 23:33:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:33:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:33:12: 7000000 INFO @ Wed, 08 Dec 2021 23:33:14: 1000000 INFO @ Wed, 08 Dec 2021 23:33:16: 8000000 INFO @ Wed, 08 Dec 2021 23:33:18: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:33:18: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:33:18: #1 total tags in treatment: 8248654 INFO @ Wed, 08 Dec 2021 23:33:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:33:18: #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 23:33:18: #1 tags after filtering in treatment: 8248654 INFO @ Wed, 08 Dec 2021 23:33:18: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:33:18: #1 finished! INFO @ Wed, 08 Dec 2021 23:33:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:33:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:33:18: #2 number of paired peaks: 404 WARNING @ Wed, 08 Dec 2021 23:33:18: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Wed, 08 Dec 2021 23:33:18: start model_add_line... INFO @ Wed, 08 Dec 2021 23:33:18: start X-correlation... INFO @ Wed, 08 Dec 2021 23:33:18: end of X-cor INFO @ Wed, 08 Dec 2021 23:33:18: #2 finished! INFO @ Wed, 08 Dec 2021 23:33:18: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 23:33:18: #2 alternative fragment length(s) may be 4,48,598 bps INFO @ Wed, 08 Dec 2021 23:33:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.05_model.r WARNING @ Wed, 08 Dec 2021 23:33:18: #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 23:33:18: #2 You may need to consider one of the other alternative d(s): 4,48,598 WARNING @ Wed, 08 Dec 2021 23:33:18: #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 23:33:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:33:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:33:19: 2000000 INFO @ Wed, 08 Dec 2021 23:33:23: 3000000 INFO @ Wed, 08 Dec 2021 23:33:28: 4000000 INFO @ Wed, 08 Dec 2021 23:33:33: 5000000 INFO @ Wed, 08 Dec 2021 23:33:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:33:37: 6000000 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 23:33:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.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 23:33:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:33:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:33:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:33:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:33:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.05_summits.bed INFO @ Wed, 08 Dec 2021 23:33:42: Done! INFO @ Wed, 08 Dec 2021 23:33:42: 7000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (639 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:33:44: 1000000 INFO @ Wed, 08 Dec 2021 23:33:47: 8000000 INFO @ Wed, 08 Dec 2021 23:33:48: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:33:48: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:33:48: #1 total tags in treatment: 8248654 INFO @ Wed, 08 Dec 2021 23:33:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:33:48: #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 23:33:48: #1 tags after filtering in treatment: 8248654 INFO @ Wed, 08 Dec 2021 23:33:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:33:48: #1 finished! INFO @ Wed, 08 Dec 2021 23:33:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:33:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:33:49: #2 number of paired peaks: 404 WARNING @ Wed, 08 Dec 2021 23:33:49: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Wed, 08 Dec 2021 23:33:49: start model_add_line... INFO @ Wed, 08 Dec 2021 23:33:49: start X-correlation... INFO @ Wed, 08 Dec 2021 23:33:49: end of X-cor INFO @ Wed, 08 Dec 2021 23:33:49: #2 finished! INFO @ Wed, 08 Dec 2021 23:33:49: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 23:33:49: #2 alternative fragment length(s) may be 4,48,598 bps INFO @ Wed, 08 Dec 2021 23:33:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.10_model.r INFO @ Wed, 08 Dec 2021 23:33:49: 2000000 WARNING @ Wed, 08 Dec 2021 23:33:49: #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 23:33:49: #2 You may need to consider one of the other alternative d(s): 4,48,598 WARNING @ Wed, 08 Dec 2021 23:33:49: #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 23:33:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:33:54: 3000000 INFO @ Wed, 08 Dec 2021 23:33:58: 4000000 INFO @ Wed, 08 Dec 2021 23:34:03: 5000000 INFO @ Wed, 08 Dec 2021 23:34:05: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:34:08: 6000000 INFO @ Wed, 08 Dec 2021 23:34:12: 7000000 INFO @ Wed, 08 Dec 2021 23:34:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:34:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:34:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.10_summits.bed INFO @ Wed, 08 Dec 2021 23:34:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (445 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:34:17: 8000000 INFO @ Wed, 08 Dec 2021 23:34:18: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:34:18: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:34:18: #1 total tags in treatment: 8248654 INFO @ Wed, 08 Dec 2021 23:34:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:34:18: #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 23:34:18: #1 tags after filtering in treatment: 8248654 INFO @ Wed, 08 Dec 2021 23:34:18: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:34:18: #1 finished! INFO @ Wed, 08 Dec 2021 23:34:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:34:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:34:19: #2 number of paired peaks: 404 WARNING @ Wed, 08 Dec 2021 23:34:19: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Wed, 08 Dec 2021 23:34:19: start model_add_line... INFO @ Wed, 08 Dec 2021 23:34:19: start X-correlation... INFO @ Wed, 08 Dec 2021 23:34:19: end of X-cor INFO @ Wed, 08 Dec 2021 23:34:19: #2 finished! INFO @ Wed, 08 Dec 2021 23:34:19: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 23:34:19: #2 alternative fragment length(s) may be 4,48,598 bps INFO @ Wed, 08 Dec 2021 23:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.20_model.r WARNING @ Wed, 08 Dec 2021 23:34:19: #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 23:34:19: #2 You may need to consider one of the other alternative d(s): 4,48,598 WARNING @ Wed, 08 Dec 2021 23:34:19: #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 23:34:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:34:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:34:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:34:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180783/SRX3180783.20_summits.bed INFO @ Wed, 08 Dec 2021 23:34:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (191 records, 4 fields): 2 millis CompletedMACS2peakCalling