Job ID = 16434967 SRX = SRX10435535 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18842116 spots for SRR14060935/SRR14060935.sra Written 18842116 spots for SRR14060935/SRR14060935.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435018 ("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: 00:05:43 18842116 reads; of these: 18842116 (100.00%) were unpaired; of these: 4241487 (22.51%) aligned 0 times 12319415 (65.38%) aligned exactly 1 time 2281214 (12.11%) aligned >1 times 77.49% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 2076177 / 14600629 = 0.1422 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 10:32:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.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 10:32:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:32:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:32:22: 1000000 INFO @ Tue, 02 Aug 2022 10:32:28: 2000000 INFO @ Tue, 02 Aug 2022 10:32:34: 3000000 INFO @ Tue, 02 Aug 2022 10:32:40: 4000000 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 10:32:46: 5000000 INFO @ Tue, 02 Aug 2022 10:32:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.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 10:32:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:32:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:32:53: 6000000 INFO @ Tue, 02 Aug 2022 10:32:53: 1000000 INFO @ Tue, 02 Aug 2022 10:32:59: 7000000 INFO @ Tue, 02 Aug 2022 10:33:00: 2000000 INFO @ Tue, 02 Aug 2022 10:33:06: 8000000 INFO @ Tue, 02 Aug 2022 10:33:07: 3000000 INFO @ Tue, 02 Aug 2022 10:33:13: 9000000 INFO @ Tue, 02 Aug 2022 10:33:14: 4000000 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 10:33:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.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 10:33:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:33:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:33:21: 10000000 INFO @ Tue, 02 Aug 2022 10:33:22: 5000000 INFO @ Tue, 02 Aug 2022 10:33:25: 1000000 INFO @ Tue, 02 Aug 2022 10:33:28: 11000000 INFO @ Tue, 02 Aug 2022 10:33:29: 6000000 INFO @ Tue, 02 Aug 2022 10:33:34: 2000000 INFO @ Tue, 02 Aug 2022 10:33:36: 12000000 INFO @ Tue, 02 Aug 2022 10:33:37: 7000000 INFO @ Tue, 02 Aug 2022 10:33:40: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:33:40: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:33:40: #1 total tags in treatment: 12524452 INFO @ Tue, 02 Aug 2022 10:33:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:33:40: #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 10:33:40: #1 tags after filtering in treatment: 12524452 INFO @ Tue, 02 Aug 2022 10:33:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:33:40: #1 finished! INFO @ Tue, 02 Aug 2022 10:33:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:33:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:33:41: #2 number of paired peaks: 698 WARNING @ Tue, 02 Aug 2022 10:33:41: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Tue, 02 Aug 2022 10:33:41: start model_add_line... INFO @ Tue, 02 Aug 2022 10:33:41: start X-correlation... INFO @ Tue, 02 Aug 2022 10:33:41: end of X-cor INFO @ Tue, 02 Aug 2022 10:33:41: #2 finished! INFO @ Tue, 02 Aug 2022 10:33:41: #2 predicted fragment length is 140 bps INFO @ Tue, 02 Aug 2022 10:33:41: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 02 Aug 2022 10:33:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.05_model.r WARNING @ Tue, 02 Aug 2022 10:33:41: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:33:41: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Tue, 02 Aug 2022 10:33:41: #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 10:33:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:33:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:33:42: 3000000 INFO @ Tue, 02 Aug 2022 10:33:45: 8000000 INFO @ Tue, 02 Aug 2022 10:33:51: 4000000 INFO @ Tue, 02 Aug 2022 10:33:52: 9000000 INFO @ Tue, 02 Aug 2022 10:34:00: 5000000 INFO @ Tue, 02 Aug 2022 10:34:00: 10000000 INFO @ Tue, 02 Aug 2022 10:34:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:34:07: 11000000 INFO @ Tue, 02 Aug 2022 10:34:08: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:34:15: 12000000 INFO @ Tue, 02 Aug 2022 10:34:17: 7000000 INFO @ Tue, 02 Aug 2022 10:34:19: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:34:19: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:34:19: #1 total tags in treatment: 12524452 INFO @ Tue, 02 Aug 2022 10:34:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:34:19: #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 10:34:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:34:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:34:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.05_summits.bed INFO @ Tue, 02 Aug 2022 10:34:19: #1 tags after filtering in treatment: 12524452 INFO @ Tue, 02 Aug 2022 10:34:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:34:19: #1 finished! INFO @ Tue, 02 Aug 2022 10:34:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:34:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:34:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2946 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:34:20: #2 number of paired peaks: 698 WARNING @ Tue, 02 Aug 2022 10:34:20: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Tue, 02 Aug 2022 10:34:20: start model_add_line... INFO @ Tue, 02 Aug 2022 10:34:20: start X-correlation... INFO @ Tue, 02 Aug 2022 10:34:20: end of X-cor INFO @ Tue, 02 Aug 2022 10:34:20: #2 finished! INFO @ Tue, 02 Aug 2022 10:34:20: #2 predicted fragment length is 140 bps INFO @ Tue, 02 Aug 2022 10:34:20: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 02 Aug 2022 10:34:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.10_model.r WARNING @ Tue, 02 Aug 2022 10:34:20: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:34:20: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Tue, 02 Aug 2022 10:34:20: #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 10:34:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:34:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:34:25: 8000000 INFO @ Tue, 02 Aug 2022 10:34:33: 9000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:34:40: 10000000 INFO @ Tue, 02 Aug 2022 10:34:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:34:48: 11000000 INFO @ Tue, 02 Aug 2022 10:34:56: 12000000 INFO @ Tue, 02 Aug 2022 10:34:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:34:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:34:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.10_summits.bed INFO @ Tue, 02 Aug 2022 10:34:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1740 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:35:00: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:35:00: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:35:00: #1 total tags in treatment: 12524452 INFO @ Tue, 02 Aug 2022 10:35:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:35:00: #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 10:35:00: #1 tags after filtering in treatment: 12524452 INFO @ Tue, 02 Aug 2022 10:35:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:35:00: #1 finished! INFO @ Tue, 02 Aug 2022 10:35:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:35:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:35:01: #2 number of paired peaks: 698 WARNING @ Tue, 02 Aug 2022 10:35:01: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Tue, 02 Aug 2022 10:35:01: start model_add_line... INFO @ Tue, 02 Aug 2022 10:35:01: start X-correlation... INFO @ Tue, 02 Aug 2022 10:35:01: end of X-cor INFO @ Tue, 02 Aug 2022 10:35:01: #2 finished! INFO @ Tue, 02 Aug 2022 10:35:01: #2 predicted fragment length is 140 bps INFO @ Tue, 02 Aug 2022 10:35:01: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 02 Aug 2022 10:35:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.20_model.r WARNING @ Tue, 02 Aug 2022 10:35:01: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:35:01: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Tue, 02 Aug 2022 10:35:01: #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 10:35:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:35:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:35:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:35:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:35:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:35:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435535/SRX10435535.20_summits.bed INFO @ Tue, 02 Aug 2022 10:35:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1005 records, 4 fields): 33 millis CompletedMACS2peakCalling