Job ID = 14160627 SRX = SRX11322241 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-08T18:27:30 prefetch.2.10.7: 1) Downloading 'SRR15010068'... 2021-12-08T18:27:30 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T18:30:36 prefetch.2.10.7: HTTPS download succeed 2021-12-08T18:30:37 prefetch.2.10.7: 'SRR15010068' is valid 2021-12-08T18:30:37 prefetch.2.10.7: 1) 'SRR15010068' was downloaded successfully 2021-12-08T18:30:37 prefetch.2.10.7: 'SRR15010068' has 0 unresolved dependencies Read 8439153 spots for SRR15010068/SRR15010068.sra Written 8439153 spots for SRR15010068/SRR15010068.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160772 ("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: 00:07:15 8439153 reads; of these: 8439153 (100.00%) were unpaired; of these: 2382680 (28.23%) aligned 0 times 5193377 (61.54%) aligned exactly 1 time 863096 (10.23%) aligned >1 times 71.77% overall alignment rate Time searching: 00:07:16 Overall time: 00:07:16 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 8 files... [bam_rmdupse_core] 918740 / 6056473 = 0.1517 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 03:42:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.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 03:42:36: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:42:36: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:42:51: 1000000 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 03:43:05: 2000000 INFO @ Thu, 09 Dec 2021 03:43:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.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 03:43:06: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:43:06: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:43:20: 3000000 INFO @ Thu, 09 Dec 2021 03:43:22: 1000000 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 03:43:35: 4000000 INFO @ Thu, 09 Dec 2021 03:43:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.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 03:43:35: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:43:35: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:43:39: 2000000 INFO @ Thu, 09 Dec 2021 03:43:50: 5000000 INFO @ Thu, 09 Dec 2021 03:43:51: 1000000 INFO @ Thu, 09 Dec 2021 03:43:52: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:43:52: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:43:52: #1 total tags in treatment: 5137733 INFO @ Thu, 09 Dec 2021 03:43:52: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:43:52: #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 03:43:52: #1 tags after filtering in treatment: 5137733 INFO @ Thu, 09 Dec 2021 03:43:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:43:52: #1 finished! INFO @ Thu, 09 Dec 2021 03:43:52: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:43:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:43:53: #2 number of paired peaks: 392 WARNING @ Thu, 09 Dec 2021 03:43:53: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Thu, 09 Dec 2021 03:43:53: start model_add_line... INFO @ Thu, 09 Dec 2021 03:43:53: start X-correlation... INFO @ Thu, 09 Dec 2021 03:43:53: end of X-cor INFO @ Thu, 09 Dec 2021 03:43:53: #2 finished! INFO @ Thu, 09 Dec 2021 03:43:53: #2 predicted fragment length is 146 bps INFO @ Thu, 09 Dec 2021 03:43:53: #2 alternative fragment length(s) may be 146,539 bps INFO @ Thu, 09 Dec 2021 03:43:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.05_model.r WARNING @ Thu, 09 Dec 2021 03:43:53: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:43:53: #2 You may need to consider one of the other alternative d(s): 146,539 WARNING @ Thu, 09 Dec 2021 03:43:53: #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 03:43:53: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:43:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:43:55: 3000000 INFO @ Thu, 09 Dec 2021 03:44:04: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:44:05: 2000000 INFO @ Thu, 09 Dec 2021 03:44:09: 4000000 INFO @ Thu, 09 Dec 2021 03:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.05_summits.bed INFO @ Thu, 09 Dec 2021 03:44:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (378 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:44:19: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:44:23: 5000000 INFO @ Thu, 09 Dec 2021 03:44:25: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:44:25: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:44:25: #1 total tags in treatment: 5137733 INFO @ Thu, 09 Dec 2021 03:44:25: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:44:25: #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 03:44:25: #1 tags after filtering in treatment: 5137733 INFO @ Thu, 09 Dec 2021 03:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:44:25: #1 finished! INFO @ Thu, 09 Dec 2021 03:44:25: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:44:25: #2 number of paired peaks: 392 WARNING @ Thu, 09 Dec 2021 03:44:25: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Thu, 09 Dec 2021 03:44:25: start model_add_line... INFO @ Thu, 09 Dec 2021 03:44:25: start X-correlation... INFO @ Thu, 09 Dec 2021 03:44:25: end of X-cor INFO @ Thu, 09 Dec 2021 03:44:25: #2 finished! INFO @ Thu, 09 Dec 2021 03:44:25: #2 predicted fragment length is 146 bps INFO @ Thu, 09 Dec 2021 03:44:25: #2 alternative fragment length(s) may be 146,539 bps INFO @ Thu, 09 Dec 2021 03:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.10_model.r WARNING @ Thu, 09 Dec 2021 03:44:25: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:44:25: #2 You may need to consider one of the other alternative d(s): 146,539 WARNING @ Thu, 09 Dec 2021 03:44:25: #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 03:44:25: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:44:34: 4000000 INFO @ Thu, 09 Dec 2021 03:44:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:44:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:44:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:44:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.10_summits.bed INFO @ Thu, 09 Dec 2021 03:44:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (275 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:44:48: 5000000 INFO @ Thu, 09 Dec 2021 03:44:49: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:44:49: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:44:49: #1 total tags in treatment: 5137733 INFO @ Thu, 09 Dec 2021 03:44:49: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:44:49: #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 03:44:49: #1 tags after filtering in treatment: 5137733 INFO @ Thu, 09 Dec 2021 03:44:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:44:49: #1 finished! INFO @ Thu, 09 Dec 2021 03:44:49: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:44:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:44:50: #2 number of paired peaks: 392 WARNING @ Thu, 09 Dec 2021 03:44:50: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Thu, 09 Dec 2021 03:44:50: start model_add_line... INFO @ Thu, 09 Dec 2021 03:44:50: start X-correlation... INFO @ Thu, 09 Dec 2021 03:44:50: end of X-cor INFO @ Thu, 09 Dec 2021 03:44:50: #2 finished! INFO @ Thu, 09 Dec 2021 03:44:50: #2 predicted fragment length is 146 bps INFO @ Thu, 09 Dec 2021 03:44:50: #2 alternative fragment length(s) may be 146,539 bps INFO @ Thu, 09 Dec 2021 03:44:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.20_model.r WARNING @ Thu, 09 Dec 2021 03:44:50: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:44:50: #2 You may need to consider one of the other alternative d(s): 146,539 WARNING @ Thu, 09 Dec 2021 03:44:50: #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 03:44:50: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:44:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:45:01: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:45:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:45:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:45:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11322241/SRX11322241.20_summits.bed INFO @ Thu, 09 Dec 2021 03:45:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (183 records, 4 fields): 2 millis CompletedMACS2peakCalling