Job ID = 6626405 SRX = SRX7262235 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 1909720 spots for SRR10581858/SRR10581858.sra Written 1909720 spots for SRR10581858/SRR10581858.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626433 ("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: 00:00:21 1909720 reads; of these: 1909720 (100.00%) were unpaired; of these: 581142 (30.43%) aligned 0 times 1063063 (55.67%) aligned exactly 1 time 265515 (13.90%) aligned >1 times 69.57% overall alignment rate Time searching: 00:00:21 Overall time: 00:00:21 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] 536432 / 1328578 = 0.4038 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 06:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.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 06:58:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:58:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:01: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:59:01: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:59:01: #1 total tags in treatment: 792146 INFO @ Tue, 14 Jul 2020 06:59:01: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:59:01: #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 06:59:01: #1 tags after filtering in treatment: 792146 INFO @ Tue, 14 Jul 2020 06:59:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:59:01: #1 finished! INFO @ Tue, 14 Jul 2020 06:59:01: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:59:01: #2 number of paired peaks: 601 WARNING @ Tue, 14 Jul 2020 06:59:01: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Tue, 14 Jul 2020 06:59:01: start model_add_line... INFO @ Tue, 14 Jul 2020 06:59:01: start X-correlation... INFO @ Tue, 14 Jul 2020 06:59:01: end of X-cor INFO @ Tue, 14 Jul 2020 06:59:01: #2 finished! INFO @ Tue, 14 Jul 2020 06:59:01: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 06:59:01: #2 alternative fragment length(s) may be 50,203,225,378,400,488 bps INFO @ Tue, 14 Jul 2020 06:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.05_model.r WARNING @ Tue, 14 Jul 2020 06:59:01: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:59:01: #2 You may need to consider one of the other alternative d(s): 50,203,225,378,400,488 WARNING @ Tue, 14 Jul 2020 06:59:01: #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 06:59:01: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 06:59:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.05_peaks.xls INFO @ Tue, 14 Jul 2020 06:59:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:59:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.05_summits.bed INFO @ Tue, 14 Jul 2020 06:59:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (310 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 06:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.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 06:59:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:33: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:59:33: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:59:33: #1 total tags in treatment: 792146 INFO @ Tue, 14 Jul 2020 06:59:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:59:33: #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 06:59:33: #1 tags after filtering in treatment: 792146 INFO @ Tue, 14 Jul 2020 06:59:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:59:33: #1 finished! INFO @ Tue, 14 Jul 2020 06:59:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:59:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:59:33: #2 number of paired peaks: 601 WARNING @ Tue, 14 Jul 2020 06:59:33: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Tue, 14 Jul 2020 06:59:33: start model_add_line... INFO @ Tue, 14 Jul 2020 06:59:33: start X-correlation... INFO @ Tue, 14 Jul 2020 06:59:33: end of X-cor INFO @ Tue, 14 Jul 2020 06:59:33: #2 finished! INFO @ Tue, 14 Jul 2020 06:59:33: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 06:59:33: #2 alternative fragment length(s) may be 50,203,225,378,400,488 bps INFO @ Tue, 14 Jul 2020 06:59:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.10_model.r WARNING @ Tue, 14 Jul 2020 06:59:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:59:33: #2 You may need to consider one of the other alternative d(s): 50,203,225,378,400,488 WARNING @ Tue, 14 Jul 2020 06:59:33: #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 06:59:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:59:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 06:59:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.10_peaks.xls INFO @ Tue, 14 Jul 2020 06:59:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:59:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.10_summits.bed INFO @ Tue, 14 Jul 2020 06:59:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (157 records, 4 fields): 11 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 06:59:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.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 06:59:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:56: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:00:03: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:03: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:03: #1 total tags in treatment: 792146 INFO @ Tue, 14 Jul 2020 07:00:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:03: #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 07:00:03: #1 tags after filtering in treatment: 792146 INFO @ Tue, 14 Jul 2020 07:00:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:03: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:03: #2 number of paired peaks: 601 WARNING @ Tue, 14 Jul 2020 07:00:03: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:03: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:03: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:03: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:03: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:03: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 07:00:03: #2 alternative fragment length(s) may be 50,203,225,378,400,488 bps INFO @ Tue, 14 Jul 2020 07:00:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.20_model.r WARNING @ Tue, 14 Jul 2020 07:00:03: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:03: #2 You may need to consider one of the other alternative d(s): 50,203,225,378,400,488 WARNING @ Tue, 14 Jul 2020 07:00:03: #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 07:00:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:00:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262235/SRX7262235.20_summits.bed INFO @ Tue, 14 Jul 2020 07:00:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (56 records, 4 fields): 16 millis CompletedMACS2peakCalling