Job ID = 14158115 SRX = SRX7739517 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11331809 spots for SRR11100921/SRR11100921.sra Written 11331809 spots for SRR11100921/SRR11100921.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158375 ("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: 00:01:47 11331809 reads; of these: 11331809 (100.00%) were unpaired; of these: 5396152 (47.62%) aligned 0 times 4953587 (43.71%) aligned exactly 1 time 982070 (8.67%) aligned >1 times 52.38% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 3650941 / 5935657 = 0.6151 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 14:31:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.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 14:31:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:31:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:31:52: 1000000 INFO @ Wed, 08 Dec 2021 14:31:57: 2000000 INFO @ Wed, 08 Dec 2021 14:31:59: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:31:59: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:31:59: #1 total tags in treatment: 2284716 INFO @ Wed, 08 Dec 2021 14:31:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:31:59: #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 14:31:59: #1 tags after filtering in treatment: 2284716 INFO @ Wed, 08 Dec 2021 14:31:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:31:59: #1 finished! INFO @ Wed, 08 Dec 2021 14:31:59: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:31:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:31:59: #2 number of paired peaks: 593 WARNING @ Wed, 08 Dec 2021 14:31:59: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Wed, 08 Dec 2021 14:31:59: start model_add_line... INFO @ Wed, 08 Dec 2021 14:31:59: start X-correlation... INFO @ Wed, 08 Dec 2021 14:31:59: end of X-cor INFO @ Wed, 08 Dec 2021 14:31:59: #2 finished! INFO @ Wed, 08 Dec 2021 14:31:59: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 14:31:59: #2 alternative fragment length(s) may be 48,496,511 bps INFO @ Wed, 08 Dec 2021 14:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.05_model.r WARNING @ Wed, 08 Dec 2021 14:31:59: #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 14:31:59: #2 You may need to consider one of the other alternative d(s): 48,496,511 WARNING @ Wed, 08 Dec 2021 14:31:59: #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 14:31:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:32:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:32:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:32:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:32:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.05_summits.bed INFO @ Wed, 08 Dec 2021 14:32:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (567 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 14:32:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.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 14:32:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:32:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:32:22: 1000000 INFO @ Wed, 08 Dec 2021 14:32:27: 2000000 INFO @ Wed, 08 Dec 2021 14:32:29: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:32:29: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:32:29: #1 total tags in treatment: 2284716 INFO @ Wed, 08 Dec 2021 14:32:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:32:29: #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 14:32:29: #1 tags after filtering in treatment: 2284716 INFO @ Wed, 08 Dec 2021 14:32:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:32:29: #1 finished! INFO @ Wed, 08 Dec 2021 14:32:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:32:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:32:29: #2 number of paired peaks: 593 WARNING @ Wed, 08 Dec 2021 14:32:29: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Wed, 08 Dec 2021 14:32:29: start model_add_line... INFO @ Wed, 08 Dec 2021 14:32:29: start X-correlation... INFO @ Wed, 08 Dec 2021 14:32:29: end of X-cor INFO @ Wed, 08 Dec 2021 14:32:29: #2 finished! INFO @ Wed, 08 Dec 2021 14:32:29: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 14:32:29: #2 alternative fragment length(s) may be 48,496,511 bps INFO @ Wed, 08 Dec 2021 14:32:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.10_model.r WARNING @ Wed, 08 Dec 2021 14:32:29: #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 14:32:29: #2 You may need to consider one of the other alternative d(s): 48,496,511 WARNING @ Wed, 08 Dec 2021 14:32:29: #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 14:32:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:32:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:32:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:32:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:32:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:32:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.10_summits.bed INFO @ Wed, 08 Dec 2021 14:32:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (335 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 14:32:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.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 14:32:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:32:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:32:52: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:32:58: 2000000 INFO @ Wed, 08 Dec 2021 14:32:59: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:32:59: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:32:59: #1 total tags in treatment: 2284716 INFO @ Wed, 08 Dec 2021 14:32:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:32:59: #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 14:32:59: #1 tags after filtering in treatment: 2284716 INFO @ Wed, 08 Dec 2021 14:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:32:59: #1 finished! INFO @ Wed, 08 Dec 2021 14:32:59: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:32:59: #2 number of paired peaks: 593 WARNING @ Wed, 08 Dec 2021 14:32:59: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Wed, 08 Dec 2021 14:32:59: start model_add_line... INFO @ Wed, 08 Dec 2021 14:32:59: start X-correlation... INFO @ Wed, 08 Dec 2021 14:32:59: end of X-cor INFO @ Wed, 08 Dec 2021 14:32:59: #2 finished! INFO @ Wed, 08 Dec 2021 14:32:59: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 14:32:59: #2 alternative fragment length(s) may be 48,496,511 bps INFO @ Wed, 08 Dec 2021 14:32:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.20_model.r WARNING @ Wed, 08 Dec 2021 14:32:59: #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 14:32:59: #2 You may need to consider one of the other alternative d(s): 48,496,511 WARNING @ Wed, 08 Dec 2021 14:32:59: #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 14:32:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:32:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:33:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:33:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:33:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:33:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739517/SRX7739517.20_summits.bed INFO @ Wed, 08 Dec 2021 14:33:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (126 records, 4 fields): 1 millis CompletedMACS2peakCalling