Job ID = 14159257 SRX = SRX3180807 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8458867 spots for SRR6030458/SRR6030458.sra Written 8458867 spots for SRR6030458/SRR6030458.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159450 ("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: 00:01:55 8458867 reads; of these: 8458867 (100.00%) were unpaired; of these: 2012773 (23.79%) aligned 0 times 5357640 (63.34%) aligned exactly 1 time 1088454 (12.87%) aligned >1 times 76.21% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 4791509 / 6446094 = 0.7433 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 20:34:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.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 20:34:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:34:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:34:29: 1000000 INFO @ Wed, 08 Dec 2021 20:34:35: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:34:35: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:34:35: #1 total tags in treatment: 1654585 INFO @ Wed, 08 Dec 2021 20:34:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:34:35: #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 20:34:35: #1 tags after filtering in treatment: 1654585 INFO @ Wed, 08 Dec 2021 20:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:34:35: #1 finished! INFO @ Wed, 08 Dec 2021 20:34:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:34:35: #2 number of paired peaks: 778 WARNING @ Wed, 08 Dec 2021 20:34:35: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Wed, 08 Dec 2021 20:34:35: start model_add_line... INFO @ Wed, 08 Dec 2021 20:34:35: start X-correlation... INFO @ Wed, 08 Dec 2021 20:34:35: end of X-cor INFO @ Wed, 08 Dec 2021 20:34:35: #2 finished! INFO @ Wed, 08 Dec 2021 20:34:35: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 20:34:35: #2 alternative fragment length(s) may be 52,439,474 bps INFO @ Wed, 08 Dec 2021 20:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.05_model.r WARNING @ Wed, 08 Dec 2021 20:34:35: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:34:35: #2 You may need to consider one of the other alternative d(s): 52,439,474 WARNING @ Wed, 08 Dec 2021 20:34:35: #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 20:34:35: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:34:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:34:39: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:34:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:34:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:34:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.05_summits.bed INFO @ Wed, 08 Dec 2021 20:34:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (568 records, 4 fields): 11 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 20:34:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.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 20:34:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:34:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:34:59: 1000000 INFO @ Wed, 08 Dec 2021 20:35:04: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:35:04: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:35:04: #1 total tags in treatment: 1654585 INFO @ Wed, 08 Dec 2021 20:35:04: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:35:04: #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 20:35:04: #1 tags after filtering in treatment: 1654585 INFO @ Wed, 08 Dec 2021 20:35:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:35:04: #1 finished! INFO @ Wed, 08 Dec 2021 20:35:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:35:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:35:04: #2 number of paired peaks: 778 WARNING @ Wed, 08 Dec 2021 20:35:04: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Wed, 08 Dec 2021 20:35:04: start model_add_line... INFO @ Wed, 08 Dec 2021 20:35:04: start X-correlation... INFO @ Wed, 08 Dec 2021 20:35:04: end of X-cor INFO @ Wed, 08 Dec 2021 20:35:04: #2 finished! INFO @ Wed, 08 Dec 2021 20:35:04: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 20:35:04: #2 alternative fragment length(s) may be 52,439,474 bps INFO @ Wed, 08 Dec 2021 20:35:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.10_model.r WARNING @ Wed, 08 Dec 2021 20:35:04: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:35:04: #2 You may need to consider one of the other alternative d(s): 52,439,474 WARNING @ Wed, 08 Dec 2021 20:35:04: #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 20:35:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:35:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:35:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:35:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:35:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:35:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.10_summits.bed INFO @ Wed, 08 Dec 2021 20:35:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 2 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 20:35:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.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 20:35:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:35:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:35:28: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:35:33: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:35:33: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:35:33: #1 total tags in treatment: 1654585 INFO @ Wed, 08 Dec 2021 20:35:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:35:33: #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 20:35:33: #1 tags after filtering in treatment: 1654585 INFO @ Wed, 08 Dec 2021 20:35:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:35:33: #1 finished! INFO @ Wed, 08 Dec 2021 20:35:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:35:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:35:34: #2 number of paired peaks: 778 WARNING @ Wed, 08 Dec 2021 20:35:34: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Wed, 08 Dec 2021 20:35:34: start model_add_line... INFO @ Wed, 08 Dec 2021 20:35:34: start X-correlation... INFO @ Wed, 08 Dec 2021 20:35:34: end of X-cor INFO @ Wed, 08 Dec 2021 20:35:34: #2 finished! INFO @ Wed, 08 Dec 2021 20:35:34: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 20:35:34: #2 alternative fragment length(s) may be 52,439,474 bps INFO @ Wed, 08 Dec 2021 20:35:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.20_model.r WARNING @ Wed, 08 Dec 2021 20:35:34: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:35:34: #2 You may need to consider one of the other alternative d(s): 52,439,474 WARNING @ Wed, 08 Dec 2021 20:35:34: #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 20:35:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:35:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:35:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:35:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:35:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:35:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180807/SRX3180807.20_summits.bed INFO @ Wed, 08 Dec 2021 20:35:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (132 records, 4 fields): 1 millis CompletedMACS2peakCalling