Job ID = 14160578 SRX = SRX10399021 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8400752 spots for SRR14022409/SRR14022409.sra Written 8400752 spots for SRR14022409/SRR14022409.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160696 ("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: 00:02:05 8400752 reads; of these: 8400752 (100.00%) were unpaired; of these: 76952 (0.92%) aligned 0 times 7041663 (83.82%) aligned exactly 1 time 1282137 (15.26%) aligned >1 times 99.08% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 595578 / 8323800 = 0.0716 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 @ Thu, 09 Dec 2021 03:20:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.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 @ Thu, 09 Dec 2021 03:20:54: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:20:54: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:21:00: 1000000 INFO @ Thu, 09 Dec 2021 03:21:07: 2000000 INFO @ Thu, 09 Dec 2021 03:21:13: 3000000 INFO @ Thu, 09 Dec 2021 03:21:19: 4000000 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 @ Thu, 09 Dec 2021 03:21:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.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 @ Thu, 09 Dec 2021 03:21:24: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:21:24: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:21:26: 5000000 INFO @ Thu, 09 Dec 2021 03:21:30: 1000000 INFO @ Thu, 09 Dec 2021 03:21:32: 6000000 INFO @ Thu, 09 Dec 2021 03:21:36: 2000000 INFO @ Thu, 09 Dec 2021 03:21:39: 7000000 INFO @ Thu, 09 Dec 2021 03:21:42: 3000000 INFO @ Thu, 09 Dec 2021 03:21:44: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:21:44: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:21:44: #1 total tags in treatment: 7728222 INFO @ Thu, 09 Dec 2021 03:21:44: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:21:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:21:44: #1 tags after filtering in treatment: 7728222 INFO @ Thu, 09 Dec 2021 03:21:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:21:44: #1 finished! INFO @ Thu, 09 Dec 2021 03:21:44: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:21:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:21:44: #2 number of paired peaks: 318 WARNING @ Thu, 09 Dec 2021 03:21:44: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Thu, 09 Dec 2021 03:21:44: start model_add_line... INFO @ Thu, 09 Dec 2021 03:21:44: start X-correlation... INFO @ Thu, 09 Dec 2021 03:21:44: end of X-cor INFO @ Thu, 09 Dec 2021 03:21:44: #2 finished! INFO @ Thu, 09 Dec 2021 03:21:44: #2 predicted fragment length is 50 bps INFO @ Thu, 09 Dec 2021 03:21:44: #2 alternative fragment length(s) may be 4,50,521,556,582 bps INFO @ Thu, 09 Dec 2021 03:21:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.05_model.r WARNING @ Thu, 09 Dec 2021 03:21:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:21:44: #2 You may need to consider one of the other alternative d(s): 4,50,521,556,582 WARNING @ Thu, 09 Dec 2021 03:21:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:21:44: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:21:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:21:47: 4000000 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 @ Thu, 09 Dec 2021 03:21:53: 5000000 INFO @ Thu, 09 Dec 2021 03:21:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.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 @ Thu, 09 Dec 2021 03:21:54: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:21:54: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:21:59: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:21:59: 6000000 INFO @ Thu, 09 Dec 2021 03:22:00: 1000000 INFO @ Thu, 09 Dec 2021 03:22:05: 7000000 INFO @ Thu, 09 Dec 2021 03:22:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:22:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:22:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.05_summits.bed INFO @ Thu, 09 Dec 2021 03:22:06: Done! pass1 - making usageList (7 chroms): 0 millis INFO @ Thu, 09 Dec 2021 03:22:07: 2000000 pass2 - checking and writing primary data (508 records, 4 fields): 1863 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:22:09: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:22:09: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:22:09: #1 total tags in treatment: 7728222 INFO @ Thu, 09 Dec 2021 03:22:09: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:22:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:22:09: #1 tags after filtering in treatment: 7728222 INFO @ Thu, 09 Dec 2021 03:22:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:22:09: #1 finished! INFO @ Thu, 09 Dec 2021 03:22:09: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:22:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:22:10: #2 number of paired peaks: 318 WARNING @ Thu, 09 Dec 2021 03:22:10: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Thu, 09 Dec 2021 03:22:10: start model_add_line... INFO @ Thu, 09 Dec 2021 03:22:10: start X-correlation... INFO @ Thu, 09 Dec 2021 03:22:10: end of X-cor INFO @ Thu, 09 Dec 2021 03:22:10: #2 finished! INFO @ Thu, 09 Dec 2021 03:22:10: #2 predicted fragment length is 50 bps INFO @ Thu, 09 Dec 2021 03:22:10: #2 alternative fragment length(s) may be 4,50,521,556,582 bps INFO @ Thu, 09 Dec 2021 03:22:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.10_model.r WARNING @ Thu, 09 Dec 2021 03:22:10: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:22:10: #2 You may need to consider one of the other alternative d(s): 4,50,521,556,582 WARNING @ Thu, 09 Dec 2021 03:22:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:22:10: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:22:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:22:13: 3000000 INFO @ Thu, 09 Dec 2021 03:22:19: 4000000 INFO @ Thu, 09 Dec 2021 03:22:24: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:22:25: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:22:30: 6000000 INFO @ Thu, 09 Dec 2021 03:22:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:22:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:22:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.10_summits.bed INFO @ Thu, 09 Dec 2021 03:22:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (301 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:22:36: 7000000 INFO @ Thu, 09 Dec 2021 03:22:40: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:22:40: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:22:40: #1 total tags in treatment: 7728222 INFO @ Thu, 09 Dec 2021 03:22:40: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:22:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:22:40: #1 tags after filtering in treatment: 7728222 INFO @ Thu, 09 Dec 2021 03:22:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:22:40: #1 finished! INFO @ Thu, 09 Dec 2021 03:22:40: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:22:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:22:40: #2 number of paired peaks: 318 WARNING @ Thu, 09 Dec 2021 03:22:40: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Thu, 09 Dec 2021 03:22:40: start model_add_line... INFO @ Thu, 09 Dec 2021 03:22:41: start X-correlation... INFO @ Thu, 09 Dec 2021 03:22:41: end of X-cor INFO @ Thu, 09 Dec 2021 03:22:41: #2 finished! INFO @ Thu, 09 Dec 2021 03:22:41: #2 predicted fragment length is 50 bps INFO @ Thu, 09 Dec 2021 03:22:41: #2 alternative fragment length(s) may be 4,50,521,556,582 bps INFO @ Thu, 09 Dec 2021 03:22:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.20_model.r WARNING @ Thu, 09 Dec 2021 03:22:41: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:22:41: #2 You may need to consider one of the other alternative d(s): 4,50,521,556,582 WARNING @ Thu, 09 Dec 2021 03:22:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:22:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:22:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:22:56: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:23:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:23:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:23:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399021/SRX10399021.20_summits.bed INFO @ Thu, 09 Dec 2021 03:23:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 1 millis CompletedMACS2peakCalling