Job ID = 6626371 SRX = SRX7262211 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 10280426 spots for SRR10581834/SRR10581834.sra Written 10280426 spots for SRR10581834/SRR10581834.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626467 ("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: 00:02:09 10280426 reads; of these: 10280426 (100.00%) were unpaired; of these: 1546261 (15.04%) aligned 0 times 6462198 (62.86%) aligned exactly 1 time 2271967 (22.10%) aligned >1 times 84.96% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 6618723 / 8734165 = 0.7578 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 07:01:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.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 07:01:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:01:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:11: 1000000 INFO @ Tue, 14 Jul 2020 07:01:16: 2000000 INFO @ Tue, 14 Jul 2020 07:01:17: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:17: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:17: #1 total tags in treatment: 2115442 INFO @ Tue, 14 Jul 2020 07:01:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:17: #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 07:01:17: #1 tags after filtering in treatment: 2115442 INFO @ Tue, 14 Jul 2020 07:01:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:17: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:17: #2 number of paired peaks: 2264 INFO @ Tue, 14 Jul 2020 07:01:17: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:17: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:17: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:17: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:17: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 07:01:17: #2 alternative fragment length(s) may be 4,56 bps INFO @ Tue, 14 Jul 2020 07:01:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.05_model.r WARNING @ Tue, 14 Jul 2020 07:01:17: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:01:17: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Tue, 14 Jul 2020 07:01:17: #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 07:01:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:01:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.05_summits.bed INFO @ Tue, 14 Jul 2020 07:01:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1071 records, 4 fields): 17 millis CompletedMACS2peakCalling 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 07:01:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.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 07:01:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:01:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:41: 1000000 INFO @ Tue, 14 Jul 2020 07:01:47: 2000000 INFO @ Tue, 14 Jul 2020 07:01:48: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:48: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:48: #1 total tags in treatment: 2115442 INFO @ Tue, 14 Jul 2020 07:01:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:48: #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 07:01:48: #1 tags after filtering in treatment: 2115442 INFO @ Tue, 14 Jul 2020 07:01:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:48: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:48: #2 number of paired peaks: 2264 INFO @ Tue, 14 Jul 2020 07:01:48: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:48: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:48: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:48: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:48: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 07:01:48: #2 alternative fragment length(s) may be 4,56 bps INFO @ Tue, 14 Jul 2020 07:01:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.10_model.r WARNING @ Tue, 14 Jul 2020 07:01:48: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:01:48: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Tue, 14 Jul 2020 07:01:48: #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 07:01:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:01:53: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.10_summits.bed INFO @ Tue, 14 Jul 2020 07:01:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (466 records, 4 fields): 13 millis CompletedMACS2peakCalling 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 07:02:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.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 07:02:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:02:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:02:11: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:02:18: 2000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:02:19: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:02:19: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:02:19: #1 total tags in treatment: 2115442 INFO @ Tue, 14 Jul 2020 07:02:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:02:19: #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 07:02:19: #1 tags after filtering in treatment: 2115442 INFO @ Tue, 14 Jul 2020 07:02:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:02:19: #1 finished! INFO @ Tue, 14 Jul 2020 07:02:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:02:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:02:19: #2 number of paired peaks: 2264 INFO @ Tue, 14 Jul 2020 07:02:19: start model_add_line... INFO @ Tue, 14 Jul 2020 07:02:19: start X-correlation... INFO @ Tue, 14 Jul 2020 07:02:19: end of X-cor INFO @ Tue, 14 Jul 2020 07:02:19: #2 finished! INFO @ Tue, 14 Jul 2020 07:02:19: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 07:02:19: #2 alternative fragment length(s) may be 4,56 bps INFO @ Tue, 14 Jul 2020 07:02:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.20_model.r WARNING @ Tue, 14 Jul 2020 07:02:19: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:02:19: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Tue, 14 Jul 2020 07:02:19: #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 07:02:19: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:02:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:02:24: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:02:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:02:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:02:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262211/SRX7262211.20_summits.bed INFO @ Tue, 14 Jul 2020 07:02:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (192 records, 4 fields): 13 millis CompletedMACS2peakCalling