Job ID = 14159383 SRX = SRX3180830 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 32694956 spots for SRR6030481/SRR6030481.sra Written 32694956 spots for SRR6030481/SRR6030481.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159592 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:05 32694956 reads; of these: 32694956 (100.00%) were unpaired; of these: 10615697 (32.47%) aligned 0 times 18440728 (56.40%) aligned exactly 1 time 3638531 (11.13%) aligned >1 times 67.53% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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_sort_core] merging from 12 files... [bam_rmdupse_core] 18021254 / 22079259 = 0.8162 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 21:38:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.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 21:38:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:38:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:38:43: 1000000 INFO @ Wed, 08 Dec 2021 21:38:50: 2000000 INFO @ Wed, 08 Dec 2021 21:38:58: 3000000 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 21:39:05: 4000000 INFO @ Wed, 08 Dec 2021 21:39:05: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:39:05: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:39:05: #1 total tags in treatment: 4058005 INFO @ Wed, 08 Dec 2021 21:39:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:39:05: #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 21:39:05: #1 tags after filtering in treatment: 4058005 INFO @ Wed, 08 Dec 2021 21:39:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:39:05: #1 finished! INFO @ Wed, 08 Dec 2021 21:39:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:39:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:39:06: #2 number of paired peaks: 956 WARNING @ Wed, 08 Dec 2021 21:39:06: Fewer paired peaks (956) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 956 pairs to build model! INFO @ Wed, 08 Dec 2021 21:39:06: start model_add_line... INFO @ Wed, 08 Dec 2021 21:39:06: start X-correlation... INFO @ Wed, 08 Dec 2021 21:39:06: end of X-cor INFO @ Wed, 08 Dec 2021 21:39:06: #2 finished! INFO @ Wed, 08 Dec 2021 21:39:06: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 21:39:06: #2 alternative fragment length(s) may be 4,49,550,578 bps INFO @ Wed, 08 Dec 2021 21:39:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.05_model.r WARNING @ Wed, 08 Dec 2021 21:39:06: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:39:06: #2 You may need to consider one of the other alternative d(s): 4,49,550,578 WARNING @ Wed, 08 Dec 2021 21:39:06: #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 21:39:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:39:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:39:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.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 21:39:06: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:39:06: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:39:13: 1000000 INFO @ Wed, 08 Dec 2021 21:39:14: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:39:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:39:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:39:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.05_summits.bed INFO @ Wed, 08 Dec 2021 21:39:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (874 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:39:20: 2000000 INFO @ Wed, 08 Dec 2021 21:39:27: 3000000 INFO @ Wed, 08 Dec 2021 21:39:34: 4000000 INFO @ Wed, 08 Dec 2021 21:39:34: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:39:34: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:39:34: #1 total tags in treatment: 4058005 INFO @ Wed, 08 Dec 2021 21:39:34: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:39:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換中... INFO @ Wed, 08 Dec 2021 21:39:34: #1 tags after filtering in treatment: 4058005 INFO @ Wed, 08 Dec 2021 21:39:34: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:39:34: #1 finished! INFO @ Wed, 08 Dec 2021 21:39:34: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:39:34: #2 looking for paired plus/minus strand peaks... 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 21:39:35: #2 number of paired peaks: 956 WARNING @ Wed, 08 Dec 2021 21:39:35: Fewer paired peaks (956) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 956 pairs to build model! INFO @ Wed, 08 Dec 2021 21:39:35: start model_add_line... INFO @ Wed, 08 Dec 2021 21:39:35: start X-correlation... INFO @ Wed, 08 Dec 2021 21:39:35: end of X-cor INFO @ Wed, 08 Dec 2021 21:39:35: #2 finished! INFO @ Wed, 08 Dec 2021 21:39:35: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 21:39:35: #2 alternative fragment length(s) may be 4,49,550,578 bps INFO @ Wed, 08 Dec 2021 21:39:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.10_model.r WARNING @ Wed, 08 Dec 2021 21:39:36: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:39:36: #2 You may need to consider one of the other alternative d(s): 4,49,550,578 WARNING @ Wed, 08 Dec 2021 21:39:36: #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 21:39:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:39:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:39:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.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 21:39:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:39:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:39:43: 1000000 INFO @ Wed, 08 Dec 2021 21:39:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:39:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:39:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:39:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.10_summits.bed INFO @ Wed, 08 Dec 2021 21:39:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:39:50: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:39:58: 3000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:40:05: 4000000 INFO @ Wed, 08 Dec 2021 21:40:05: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:40:05: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:40:05: #1 total tags in treatment: 4058005 INFO @ Wed, 08 Dec 2021 21:40:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:40:05: #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 21:40:05: #1 tags after filtering in treatment: 4058005 INFO @ Wed, 08 Dec 2021 21:40:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:40:05: #1 finished! INFO @ Wed, 08 Dec 2021 21:40:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:40:06: #2 number of paired peaks: 956 WARNING @ Wed, 08 Dec 2021 21:40:06: Fewer paired peaks (956) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 956 pairs to build model! INFO @ Wed, 08 Dec 2021 21:40:06: start model_add_line... INFO @ Wed, 08 Dec 2021 21:40:06: start X-correlation... INFO @ Wed, 08 Dec 2021 21:40:06: end of X-cor INFO @ Wed, 08 Dec 2021 21:40:06: #2 finished! INFO @ Wed, 08 Dec 2021 21:40:06: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 21:40:06: #2 alternative fragment length(s) may be 4,49,550,578 bps INFO @ Wed, 08 Dec 2021 21:40:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.20_model.r WARNING @ Wed, 08 Dec 2021 21:40:06: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:40:06: #2 You may need to consider one of the other alternative d(s): 4,49,550,578 WARNING @ Wed, 08 Dec 2021 21:40:06: #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 21:40:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:40:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:40:14: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:40:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:40:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:40:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180830/SRX3180830.20_summits.bed INFO @ Wed, 08 Dec 2021 21:40:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (251 records, 4 fields): 2 millis CompletedMACS2peakCalling