Job ID = 6626396 SRX = SRX7262230 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5401926 spots for SRR10581853/SRR10581853.sra Written 5401926 spots for SRR10581853/SRR10581853.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626458 ("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: 00:01:06 5401926 reads; of these: 5401926 (100.00%) were unpaired; of these: 938742 (17.38%) aligned 0 times 3560836 (65.92%) aligned exactly 1 time 902348 (16.70%) aligned >1 times 82.62% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 262173 / 4463184 = 0.0587 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:00:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.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, 14 Jul 2020 07:00:16: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:16: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:21: 1000000 INFO @ Tue, 14 Jul 2020 07:00:27: 2000000 INFO @ Tue, 14 Jul 2020 07:00:32: 3000000 INFO @ Tue, 14 Jul 2020 07:00:37: 4000000 INFO @ Tue, 14 Jul 2020 07:00:38: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:38: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:38: #1 total tags in treatment: 4201011 INFO @ Tue, 14 Jul 2020 07:00:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:00:38: #1 tags after filtering in treatment: 4201011 INFO @ Tue, 14 Jul 2020 07:00:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:38: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:38: #2 number of paired peaks: 442 WARNING @ Tue, 14 Jul 2020 07:00:38: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:38: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:38: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:38: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:38: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:38: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 07:00:38: #2 alternative fragment length(s) may be 48,484 bps INFO @ Tue, 14 Jul 2020 07:00:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.05_model.r WARNING @ Tue, 14 Jul 2020 07:00:38: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:38: #2 You may need to consider one of the other alternative d(s): 48,484 WARNING @ Tue, 14 Jul 2020 07:00:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:00:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:38: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:00:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.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, 14 Jul 2020 07:00:46: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:46: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.05_summits.bed INFO @ Tue, 14 Jul 2020 07:00:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (521 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:00:52: 1000000 INFO @ Tue, 14 Jul 2020 07:00:59: 2000000 INFO @ Tue, 14 Jul 2020 07:01:05: 3000000 INFO @ Tue, 14 Jul 2020 07:01:11: 4000000 INFO @ Tue, 14 Jul 2020 07:01:12: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:12: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:12: #1 total tags in treatment: 4201011 INFO @ Tue, 14 Jul 2020 07:01:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:01:12: #1 tags after filtering in treatment: 4201011 INFO @ Tue, 14 Jul 2020 07:01:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:12: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:12: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:12: #2 number of paired peaks: 442 WARNING @ Tue, 14 Jul 2020 07:01:12: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:12: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:12: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:12: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:12: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:12: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 07:01:12: #2 alternative fragment length(s) may be 48,484 bps INFO @ Tue, 14 Jul 2020 07:01:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.10_model.r WARNING @ Tue, 14 Jul 2020 07:01:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:01:12: #2 You may need to consider one of the other alternative d(s): 48,484 WARNING @ Tue, 14 Jul 2020 07:01:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:01:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:12: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.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, 14 Jul 2020 07:01:16: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:01:16: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:23: 1000000 INFO @ Tue, 14 Jul 2020 07:01:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.10_summits.bed INFO @ Tue, 14 Jul 2020 07:01:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (321 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:01:28: 2000000 INFO @ Tue, 14 Jul 2020 07:01:32: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:01:37: 4000000 INFO @ Tue, 14 Jul 2020 07:01:38: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:38: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:38: #1 total tags in treatment: 4201011 INFO @ Tue, 14 Jul 2020 07:01:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:01:38: #1 tags after filtering in treatment: 4201011 INFO @ Tue, 14 Jul 2020 07:01:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:38: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:38: #2 number of paired peaks: 442 WARNING @ Tue, 14 Jul 2020 07:01:38: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:38: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:38: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:38: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:38: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:38: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 07:01:38: #2 alternative fragment length(s) may be 48,484 bps INFO @ Tue, 14 Jul 2020 07:01:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.20_model.r WARNING @ Tue, 14 Jul 2020 07:01:39: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:01:39: #2 You may need to consider one of the other alternative d(s): 48,484 WARNING @ Tue, 14 Jul 2020 07:01:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:01:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:01:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262230/SRX7262230.20_summits.bed INFO @ Tue, 14 Jul 2020 07:01:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (141 records, 4 fields): 34 millis CompletedMACS2peakCalling