Job ID = 10165629 SRX = SRX6799186 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 35279189 spots for SRR10065393/SRR10065393.sra Written 35279189 spots for SRR10065393/SRR10065393.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165892 ("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: 00:07:37 35279189 reads; of these: 35279189 (100.00%) were unpaired; of these: 1633576 (4.63%) aligned 0 times 26488531 (75.08%) aligned exactly 1 time 7157082 (20.29%) aligned >1 times 95.37% overall alignment rate Time searching: 00:07:37 Overall time: 00:07:37 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 16 files... [bam_rmdupse_core] 9685316 / 33645613 = 0.2879 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:46:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.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, 08 Oct 2020 19:46:42: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:46:42: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:46:46: 1000000 INFO @ Thu, 08 Oct 2020 19:46:51: 2000000 INFO @ Thu, 08 Oct 2020 19:46:56: 3000000 INFO @ Thu, 08 Oct 2020 19:47:00: 4000000 INFO @ Thu, 08 Oct 2020 19:47:05: 5000000 INFO @ Thu, 08 Oct 2020 19:47:10: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:47:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.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, 08 Oct 2020 19:47:12: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:12: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:15: 7000000 INFO @ Thu, 08 Oct 2020 19:47:17: 1000000 INFO @ Thu, 08 Oct 2020 19:47:20: 8000000 INFO @ Thu, 08 Oct 2020 19:47:23: 2000000 INFO @ Thu, 08 Oct 2020 19:47:25: 9000000 INFO @ Thu, 08 Oct 2020 19:47:28: 3000000 INFO @ Thu, 08 Oct 2020 19:47:30: 10000000 INFO @ Thu, 08 Oct 2020 19:47:34: 4000000 INFO @ Thu, 08 Oct 2020 19:47:35: 11000000 INFO @ Thu, 08 Oct 2020 19:47:39: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:47:40: 12000000 INFO @ Thu, 08 Oct 2020 19:47:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.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, 08 Oct 2020 19:47:42: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:42: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:44: 6000000 INFO @ Thu, 08 Oct 2020 19:47:45: 13000000 INFO @ Thu, 08 Oct 2020 19:47:48: 1000000 INFO @ Thu, 08 Oct 2020 19:47:50: 7000000 INFO @ Thu, 08 Oct 2020 19:47:50: 14000000 INFO @ Thu, 08 Oct 2020 19:47:54: 2000000 INFO @ Thu, 08 Oct 2020 19:47:55: 8000000 INFO @ Thu, 08 Oct 2020 19:47:56: 15000000 INFO @ Thu, 08 Oct 2020 19:48:00: 3000000 INFO @ Thu, 08 Oct 2020 19:48:00: 9000000 INFO @ Thu, 08 Oct 2020 19:48:01: 16000000 INFO @ Thu, 08 Oct 2020 19:48:06: 10000000 INFO @ Thu, 08 Oct 2020 19:48:06: 4000000 INFO @ Thu, 08 Oct 2020 19:48:07: 17000000 INFO @ Thu, 08 Oct 2020 19:48:11: 11000000 INFO @ Thu, 08 Oct 2020 19:48:12: 5000000 INFO @ Thu, 08 Oct 2020 19:48:12: 18000000 INFO @ Thu, 08 Oct 2020 19:48:16: 12000000 INFO @ Thu, 08 Oct 2020 19:48:17: 19000000 INFO @ Thu, 08 Oct 2020 19:48:18: 6000000 INFO @ Thu, 08 Oct 2020 19:48:21: 13000000 INFO @ Thu, 08 Oct 2020 19:48:23: 20000000 INFO @ Thu, 08 Oct 2020 19:48:24: 7000000 INFO @ Thu, 08 Oct 2020 19:48:27: 14000000 INFO @ Thu, 08 Oct 2020 19:48:28: 21000000 INFO @ Thu, 08 Oct 2020 19:48:30: 8000000 INFO @ Thu, 08 Oct 2020 19:48:32: 15000000 INFO @ Thu, 08 Oct 2020 19:48:33: 22000000 INFO @ Thu, 08 Oct 2020 19:48:36: 9000000 INFO @ Thu, 08 Oct 2020 19:48:38: 16000000 INFO @ Thu, 08 Oct 2020 19:48:39: 23000000 INFO @ Thu, 08 Oct 2020 19:48:42: 10000000 INFO @ Thu, 08 Oct 2020 19:48:43: 17000000 INFO @ Thu, 08 Oct 2020 19:48:44: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:48:44: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:48:44: #1 total tags in treatment: 23960297 INFO @ Thu, 08 Oct 2020 19:48:44: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:48:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:48:44: #1 tags after filtering in treatment: 23960297 INFO @ Thu, 08 Oct 2020 19:48:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:48:44: #1 finished! INFO @ Thu, 08 Oct 2020 19:48:44: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:48:46: #2 number of paired peaks: 159 WARNING @ Thu, 08 Oct 2020 19:48:46: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Thu, 08 Oct 2020 19:48:46: start model_add_line... INFO @ Thu, 08 Oct 2020 19:48:46: start X-correlation... INFO @ Thu, 08 Oct 2020 19:48:46: end of X-cor INFO @ Thu, 08 Oct 2020 19:48:46: #2 finished! INFO @ Thu, 08 Oct 2020 19:48:46: #2 predicted fragment length is 52 bps INFO @ Thu, 08 Oct 2020 19:48:46: #2 alternative fragment length(s) may be 3,52,118,198 bps INFO @ Thu, 08 Oct 2020 19:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.05_model.r WARNING @ Thu, 08 Oct 2020 19:48:46: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:48:46: #2 You may need to consider one of the other alternative d(s): 3,52,118,198 WARNING @ Thu, 08 Oct 2020 19:48:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:48:46: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:48:48: 18000000 INFO @ Thu, 08 Oct 2020 19:48:49: 11000000 INFO @ Thu, 08 Oct 2020 19:48:54: 19000000 INFO @ Thu, 08 Oct 2020 19:48:55: 12000000 INFO @ Thu, 08 Oct 2020 19:49:00: 20000000 INFO @ Thu, 08 Oct 2020 19:49:01: 13000000 INFO @ Thu, 08 Oct 2020 19:49:05: 21000000 INFO @ Thu, 08 Oct 2020 19:49:07: 14000000 INFO @ Thu, 08 Oct 2020 19:49:11: 22000000 INFO @ Thu, 08 Oct 2020 19:49:14: 15000000 INFO @ Thu, 08 Oct 2020 19:49:16: 23000000 INFO @ Thu, 08 Oct 2020 19:49:21: 16000000 INFO @ Thu, 08 Oct 2020 19:49:21: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:49:21: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:49:21: #1 total tags in treatment: 23960297 INFO @ Thu, 08 Oct 2020 19:49:21: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:49:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:49:22: #1 tags after filtering in treatment: 23960297 INFO @ Thu, 08 Oct 2020 19:49:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:49:22: #1 finished! INFO @ Thu, 08 Oct 2020 19:49:22: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:49:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:49:23: #2 number of paired peaks: 159 WARNING @ Thu, 08 Oct 2020 19:49:23: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Thu, 08 Oct 2020 19:49:23: start model_add_line... INFO @ Thu, 08 Oct 2020 19:49:23: start X-correlation... INFO @ Thu, 08 Oct 2020 19:49:23: end of X-cor INFO @ Thu, 08 Oct 2020 19:49:23: #2 finished! INFO @ Thu, 08 Oct 2020 19:49:23: #2 predicted fragment length is 52 bps INFO @ Thu, 08 Oct 2020 19:49:23: #2 alternative fragment length(s) may be 3,52,118,198 bps INFO @ Thu, 08 Oct 2020 19:49:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.10_model.r WARNING @ Thu, 08 Oct 2020 19:49:23: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:49:23: #2 You may need to consider one of the other alternative d(s): 3,52,118,198 WARNING @ Thu, 08 Oct 2020 19:49:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:49:23: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:49:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:49:24: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:49:27: 17000000 INFO @ Thu, 08 Oct 2020 19:49:33: 18000000 INFO @ Thu, 08 Oct 2020 19:49:39: 19000000 INFO @ Thu, 08 Oct 2020 19:49:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:49:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:49:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.05_summits.bed INFO @ Thu, 08 Oct 2020 19:49:43: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9542 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:49:45: 20000000 INFO @ Thu, 08 Oct 2020 19:49:52: 21000000 INFO @ Thu, 08 Oct 2020 19:49:58: 22000000 INFO @ Thu, 08 Oct 2020 19:50:02: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:50:04: 23000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:50:09: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:50:09: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:50:09: #1 total tags in treatment: 23960297 INFO @ Thu, 08 Oct 2020 19:50:09: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:50:10: #1 tags after filtering in treatment: 23960297 INFO @ Thu, 08 Oct 2020 19:50:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:10: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:10: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:11: #2 number of paired peaks: 159 WARNING @ Thu, 08 Oct 2020 19:50:11: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:11: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:11: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:11: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:11: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:11: #2 predicted fragment length is 52 bps INFO @ Thu, 08 Oct 2020 19:50:11: #2 alternative fragment length(s) may be 3,52,118,198 bps INFO @ Thu, 08 Oct 2020 19:50:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.20_model.r WARNING @ Thu, 08 Oct 2020 19:50:11: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:50:11: #2 You may need to consider one of the other alternative d(s): 3,52,118,198 WARNING @ Thu, 08 Oct 2020 19:50:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:50:11: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.10_summits.bed INFO @ Thu, 08 Oct 2020 19:50:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2698 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:50:49: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:51:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:51:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799186/SRX6799186.20_summits.bed INFO @ Thu, 08 Oct 2020 19:51:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (391 records, 4 fields): 2 millis CompletedMACS2peakCalling