Job ID = 16434847 SRX = SRX11633387 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12818150 spots for SRR15329107/SRR15329107.sra Written 12818150 spots for SRR15329107/SRR15329107.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434894 ("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: 00:04:54 12818150 reads; of these: 12818150 (100.00%) were unpaired; of these: 1121463 (8.75%) aligned 0 times 10102966 (78.82%) aligned exactly 1 time 1593721 (12.43%) aligned >1 times 91.25% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 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] 651116 / 11696687 = 0.0557 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:15:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.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 @ Tue, 02 Aug 2022 10:15:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:15:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:15:10: 1000000 INFO @ Tue, 02 Aug 2022 10:15:18: 2000000 INFO @ Tue, 02 Aug 2022 10:15:26: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:15:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.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 @ Tue, 02 Aug 2022 10:15:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:15:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:15:34: 4000000 INFO @ Tue, 02 Aug 2022 10:15:42: 1000000 INFO @ Tue, 02 Aug 2022 10:15:42: 5000000 INFO @ Tue, 02 Aug 2022 10:15:50: 6000000 INFO @ Tue, 02 Aug 2022 10:15:53: 2000000 INFO @ Tue, 02 Aug 2022 10:15:58: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:16:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.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 @ Tue, 02 Aug 2022 10:16:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:16:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:16:03: 3000000 INFO @ Tue, 02 Aug 2022 10:16:07: 8000000 INFO @ Tue, 02 Aug 2022 10:16:12: 1000000 INFO @ Tue, 02 Aug 2022 10:16:14: 4000000 INFO @ Tue, 02 Aug 2022 10:16:15: 9000000 INFO @ Tue, 02 Aug 2022 10:16:23: 2000000 INFO @ Tue, 02 Aug 2022 10:16:23: 10000000 INFO @ Tue, 02 Aug 2022 10:16:25: 5000000 INFO @ Tue, 02 Aug 2022 10:16:32: 11000000 INFO @ Tue, 02 Aug 2022 10:16:32: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:16:32: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:16:32: #1 total tags in treatment: 11045571 INFO @ Tue, 02 Aug 2022 10:16:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:16:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:16:32: #1 tags after filtering in treatment: 11045571 INFO @ Tue, 02 Aug 2022 10:16:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:16:32: #1 finished! INFO @ Tue, 02 Aug 2022 10:16:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:16:33: #2 number of paired peaks: 212 WARNING @ Tue, 02 Aug 2022 10:16:33: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Tue, 02 Aug 2022 10:16:33: start model_add_line... INFO @ Tue, 02 Aug 2022 10:16:33: start X-correlation... INFO @ Tue, 02 Aug 2022 10:16:33: end of X-cor INFO @ Tue, 02 Aug 2022 10:16:33: #2 finished! INFO @ Tue, 02 Aug 2022 10:16:33: #2 predicted fragment length is 64 bps INFO @ Tue, 02 Aug 2022 10:16:33: #2 alternative fragment length(s) may be 3,64 bps INFO @ Tue, 02 Aug 2022 10:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.05_model.r WARNING @ Tue, 02 Aug 2022 10:16:33: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:16:33: #2 You may need to consider one of the other alternative d(s): 3,64 WARNING @ Tue, 02 Aug 2022 10:16:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:16:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:16:34: 3000000 INFO @ Tue, 02 Aug 2022 10:16:36: 6000000 INFO @ Tue, 02 Aug 2022 10:16:44: 4000000 INFO @ Tue, 02 Aug 2022 10:16:46: 7000000 INFO @ Tue, 02 Aug 2022 10:16:55: 5000000 INFO @ Tue, 02 Aug 2022 10:16:56: 8000000 INFO @ Tue, 02 Aug 2022 10:17:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:17:06: 6000000 INFO @ Tue, 02 Aug 2022 10:17:07: 9000000 INFO @ Tue, 02 Aug 2022 10:17:16: 7000000 INFO @ Tue, 02 Aug 2022 10:17:17: 10000000 INFO @ Tue, 02 Aug 2022 10:17:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:17:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:17:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.05_summits.bed INFO @ Tue, 02 Aug 2022 10:17:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:17:27: 8000000 INFO @ Tue, 02 Aug 2022 10:17:28: 11000000 INFO @ Tue, 02 Aug 2022 10:17:28: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:17:28: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:17:28: #1 total tags in treatment: 11045571 INFO @ Tue, 02 Aug 2022 10:17:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:17:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:17:28: #1 tags after filtering in treatment: 11045571 INFO @ Tue, 02 Aug 2022 10:17:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:17:28: #1 finished! INFO @ Tue, 02 Aug 2022 10:17:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:17:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:17:29: #2 number of paired peaks: 212 WARNING @ Tue, 02 Aug 2022 10:17:29: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Tue, 02 Aug 2022 10:17:29: start model_add_line... INFO @ Tue, 02 Aug 2022 10:17:30: start X-correlation... INFO @ Tue, 02 Aug 2022 10:17:30: end of X-cor INFO @ Tue, 02 Aug 2022 10:17:30: #2 finished! INFO @ Tue, 02 Aug 2022 10:17:30: #2 predicted fragment length is 64 bps INFO @ Tue, 02 Aug 2022 10:17:30: #2 alternative fragment length(s) may be 3,64 bps INFO @ Tue, 02 Aug 2022 10:17:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.10_model.r WARNING @ Tue, 02 Aug 2022 10:17:30: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:17:30: #2 You may need to consider one of the other alternative d(s): 3,64 WARNING @ Tue, 02 Aug 2022 10:17:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:17:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:17:37: 9000000 INFO @ Tue, 02 Aug 2022 10:17:48: 10000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:17:58: 11000000 INFO @ Tue, 02 Aug 2022 10:17:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:17:59: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:17:59: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:17:59: #1 total tags in treatment: 11045571 INFO @ Tue, 02 Aug 2022 10:17:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:17:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:17:59: #1 tags after filtering in treatment: 11045571 INFO @ Tue, 02 Aug 2022 10:17:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:17:59: #1 finished! INFO @ Tue, 02 Aug 2022 10:17:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:17:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:18:00: #2 number of paired peaks: 212 WARNING @ Tue, 02 Aug 2022 10:18:00: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Tue, 02 Aug 2022 10:18:00: start model_add_line... INFO @ Tue, 02 Aug 2022 10:18:00: start X-correlation... INFO @ Tue, 02 Aug 2022 10:18:00: end of X-cor INFO @ Tue, 02 Aug 2022 10:18:00: #2 finished! INFO @ Tue, 02 Aug 2022 10:18:00: #2 predicted fragment length is 64 bps INFO @ Tue, 02 Aug 2022 10:18:00: #2 alternative fragment length(s) may be 3,64 bps INFO @ Tue, 02 Aug 2022 10:18:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.20_model.r WARNING @ Tue, 02 Aug 2022 10:18:00: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:18:00: #2 You may need to consider one of the other alternative d(s): 3,64 WARNING @ Tue, 02 Aug 2022 10:18:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:18:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:18:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:18:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:18:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:18:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.10_summits.bed INFO @ Tue, 02 Aug 2022 10:18:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (292 records, 4 fields): 61 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:18:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:18:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:18:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:18:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633387/SRX11633387.20_summits.bed INFO @ Tue, 02 Aug 2022 10:18:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (149 records, 4 fields): 15 millis CompletedMACS2peakCalling