Job ID = 16434924 SRX = SRX11633394 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9798601 spots for SRR15329102/SRR15329102.sra Written 9798601 spots for SRR15329102/SRR15329102.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434977 ("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: 00:03:24 9798601 reads; of these: 9798601 (100.00%) were unpaired; of these: 996433 (10.17%) aligned 0 times 7529611 (76.84%) aligned exactly 1 time 1272557 (12.99%) aligned >1 times 89.83% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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] 3134204 / 8802168 = 0.3561 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 10:24:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.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 10:24:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:24:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:24:48: 1000000 INFO @ Tue, 02 Aug 2022 10:24:55: 2000000 INFO @ Tue, 02 Aug 2022 10:25:01: 3000000 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 10:25:08: 4000000 INFO @ Tue, 02 Aug 2022 10:25:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.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 10:25:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:25:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:25:15: 5000000 INFO @ Tue, 02 Aug 2022 10:25:17: 1000000 INFO @ Tue, 02 Aug 2022 10:25:20: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:25:20: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:25:20: #1 total tags in treatment: 5667964 INFO @ Tue, 02 Aug 2022 10:25:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:25:20: #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 10:25:20: #1 tags after filtering in treatment: 5667964 INFO @ Tue, 02 Aug 2022 10:25:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:25:20: #1 finished! INFO @ Tue, 02 Aug 2022 10:25:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:25:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:25:20: #2 number of paired peaks: 338 WARNING @ Tue, 02 Aug 2022 10:25:20: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 02 Aug 2022 10:25:20: start model_add_line... INFO @ Tue, 02 Aug 2022 10:25:21: start X-correlation... INFO @ Tue, 02 Aug 2022 10:25:21: end of X-cor INFO @ Tue, 02 Aug 2022 10:25:21: #2 finished! INFO @ Tue, 02 Aug 2022 10:25:21: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 10:25:21: #2 alternative fragment length(s) may be 69 bps INFO @ Tue, 02 Aug 2022 10:25:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.05_model.r WARNING @ Tue, 02 Aug 2022 10:25:21: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:25:21: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Tue, 02 Aug 2022 10:25:21: #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 10:25:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:25:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:25:24: 2000000 INFO @ Tue, 02 Aug 2022 10:25:31: 3000000 INFO @ Tue, 02 Aug 2022 10:25:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:25:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:25:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:25:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.05_summits.bed INFO @ Tue, 02 Aug 2022 10:25:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Tue, 02 Aug 2022 10:25:38: 4000000 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 10:25:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.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 10:25:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:25:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:25:45: 5000000 INFO @ Tue, 02 Aug 2022 10:25:48: 1000000 INFO @ Tue, 02 Aug 2022 10:25:50: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:25:50: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:25:50: #1 total tags in treatment: 5667964 INFO @ Tue, 02 Aug 2022 10:25:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:25:50: #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 10:25:51: #1 tags after filtering in treatment: 5667964 INFO @ Tue, 02 Aug 2022 10:25:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:25:51: #1 finished! INFO @ Tue, 02 Aug 2022 10:25:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:25:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:25:51: #2 number of paired peaks: 338 WARNING @ Tue, 02 Aug 2022 10:25:51: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 02 Aug 2022 10:25:51: start model_add_line... INFO @ Tue, 02 Aug 2022 10:25:51: start X-correlation... INFO @ Tue, 02 Aug 2022 10:25:51: end of X-cor INFO @ Tue, 02 Aug 2022 10:25:51: #2 finished! INFO @ Tue, 02 Aug 2022 10:25:51: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 10:25:51: #2 alternative fragment length(s) may be 69 bps INFO @ Tue, 02 Aug 2022 10:25:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.10_model.r WARNING @ Tue, 02 Aug 2022 10:25:51: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:25:51: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Tue, 02 Aug 2022 10:25:51: #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 10:25:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:25:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:25:55: 2000000 INFO @ Tue, 02 Aug 2022 10:26:02: 3000000 INFO @ Tue, 02 Aug 2022 10:26:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:26:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:26:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.10_summits.bed INFO @ Tue, 02 Aug 2022 10:26:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (246 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:26:08: 4000000 INFO @ Tue, 02 Aug 2022 10:26:15: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:26:20: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:26:20: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:26:20: #1 total tags in treatment: 5667964 INFO @ Tue, 02 Aug 2022 10:26:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:26:20: #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 10:26:20: #1 tags after filtering in treatment: 5667964 INFO @ Tue, 02 Aug 2022 10:26:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:26:20: #1 finished! INFO @ Tue, 02 Aug 2022 10:26:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:26:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:26:21: #2 number of paired peaks: 338 WARNING @ Tue, 02 Aug 2022 10:26:21: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 02 Aug 2022 10:26:21: start model_add_line... INFO @ Tue, 02 Aug 2022 10:26:21: start X-correlation... INFO @ Tue, 02 Aug 2022 10:26:21: end of X-cor INFO @ Tue, 02 Aug 2022 10:26:21: #2 finished! INFO @ Tue, 02 Aug 2022 10:26:21: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 10:26:21: #2 alternative fragment length(s) may be 69 bps INFO @ Tue, 02 Aug 2022 10:26:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.20_model.r WARNING @ Tue, 02 Aug 2022 10:26:21: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:26:21: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Tue, 02 Aug 2022 10:26:21: #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 10:26:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:26:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:26:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:26:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:26:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633394/SRX11633394.20_summits.bed INFO @ Tue, 02 Aug 2022 10:26:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 16 millis CompletedMACS2peakCalling