Job ID = 16435009 SRX = SRX10435545 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15285451 spots for SRR14060961/SRR14060961.sra Written 15285451 spots for SRR14060961/SRR14060961.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435144 ("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: 00:04:51 15285451 reads; of these: 15285451 (100.00%) were unpaired; of these: 556699 (3.64%) aligned 0 times 12182754 (79.70%) aligned exactly 1 time 2545998 (16.66%) aligned >1 times 96.36% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 1528239 / 14728752 = 0.1038 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 10:38:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.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 10:38:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:38:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:38:53: 1000000 INFO @ Tue, 02 Aug 2022 10:38:58: 2000000 INFO @ Tue, 02 Aug 2022 10:39:03: 3000000 INFO @ Tue, 02 Aug 2022 10:39:08: 4000000 INFO @ Tue, 02 Aug 2022 10:39:14: 5000000 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 10:39:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.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 10:39:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:39:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:39:19: 6000000 INFO @ Tue, 02 Aug 2022 10:39:23: 1000000 INFO @ Tue, 02 Aug 2022 10:39:25: 7000000 INFO @ Tue, 02 Aug 2022 10:39:29: 2000000 INFO @ Tue, 02 Aug 2022 10:39:31: 8000000 INFO @ Tue, 02 Aug 2022 10:39:35: 3000000 INFO @ Tue, 02 Aug 2022 10:39:37: 9000000 INFO @ Tue, 02 Aug 2022 10:39:41: 4000000 INFO @ Tue, 02 Aug 2022 10:39:43: 10000000 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 10:39:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.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 10:39:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:39:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:39:46: 5000000 INFO @ Tue, 02 Aug 2022 10:39:49: 11000000 INFO @ Tue, 02 Aug 2022 10:39:53: 6000000 INFO @ Tue, 02 Aug 2022 10:39:53: 1000000 INFO @ Tue, 02 Aug 2022 10:39:55: 12000000 INFO @ Tue, 02 Aug 2022 10:39:59: 7000000 INFO @ Tue, 02 Aug 2022 10:40:00: 2000000 INFO @ Tue, 02 Aug 2022 10:40:02: 13000000 INFO @ Tue, 02 Aug 2022 10:40:03: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:40:03: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:40:03: #1 total tags in treatment: 13200513 INFO @ Tue, 02 Aug 2022 10:40:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:40:03: #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 10:40:03: #1 tags after filtering in treatment: 13200513 INFO @ Tue, 02 Aug 2022 10:40:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:40:03: #1 finished! INFO @ Tue, 02 Aug 2022 10:40:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:40:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:40:04: #2 number of paired peaks: 301 WARNING @ Tue, 02 Aug 2022 10:40:04: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Tue, 02 Aug 2022 10:40:04: start model_add_line... INFO @ Tue, 02 Aug 2022 10:40:04: start X-correlation... INFO @ Tue, 02 Aug 2022 10:40:04: end of X-cor INFO @ Tue, 02 Aug 2022 10:40:04: #2 finished! INFO @ Tue, 02 Aug 2022 10:40:04: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:40:04: #2 alternative fragment length(s) may be 4,70 bps INFO @ Tue, 02 Aug 2022 10:40:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.05_model.r WARNING @ Tue, 02 Aug 2022 10:40:04: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:40:04: #2 You may need to consider one of the other alternative d(s): 4,70 WARNING @ Tue, 02 Aug 2022 10:40:04: #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 10:40:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:40:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:40:05: 8000000 INFO @ Tue, 02 Aug 2022 10:40:07: 3000000 INFO @ Tue, 02 Aug 2022 10:40:11: 9000000 INFO @ Tue, 02 Aug 2022 10:40:14: 4000000 INFO @ Tue, 02 Aug 2022 10:40:17: 10000000 INFO @ Tue, 02 Aug 2022 10:40:20: 5000000 INFO @ Tue, 02 Aug 2022 10:40:23: 11000000 INFO @ Tue, 02 Aug 2022 10:40:27: 6000000 INFO @ Tue, 02 Aug 2022 10:40:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:40:29: 12000000 INFO @ Tue, 02 Aug 2022 10:40:34: 7000000 INFO @ Tue, 02 Aug 2022 10:40:35: 13000000 INFO @ Tue, 02 Aug 2022 10:40:37: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:40:37: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:40:37: #1 total tags in treatment: 13200513 INFO @ Tue, 02 Aug 2022 10:40:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:40:37: #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 10:40:37: #1 tags after filtering in treatment: 13200513 INFO @ Tue, 02 Aug 2022 10:40:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:40:37: #1 finished! INFO @ Tue, 02 Aug 2022 10:40:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:40:38: #2 number of paired peaks: 301 WARNING @ Tue, 02 Aug 2022 10:40:38: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Tue, 02 Aug 2022 10:40:38: start model_add_line... INFO @ Tue, 02 Aug 2022 10:40:38: start X-correlation... INFO @ Tue, 02 Aug 2022 10:40:38: end of X-cor INFO @ Tue, 02 Aug 2022 10:40:38: #2 finished! INFO @ Tue, 02 Aug 2022 10:40:38: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:40:38: #2 alternative fragment length(s) may be 4,70 bps INFO @ Tue, 02 Aug 2022 10:40:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.10_model.r WARNING @ Tue, 02 Aug 2022 10:40:38: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:40:38: #2 You may need to consider one of the other alternative d(s): 4,70 WARNING @ Tue, 02 Aug 2022 10:40:38: #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 10:40:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:40:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:40:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:40:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:40:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.05_summits.bed INFO @ Tue, 02 Aug 2022 10:40:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (806 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:40:41: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:40:47: 9000000 INFO @ Tue, 02 Aug 2022 10:40:54: 10000000 INFO @ Tue, 02 Aug 2022 10:41:00: 11000000 INFO @ Tue, 02 Aug 2022 10:41:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:41:06: 12000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:41:13: 13000000 INFO @ Tue, 02 Aug 2022 10:41:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:41:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:41:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.10_summits.bed INFO @ Tue, 02 Aug 2022 10:41:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (454 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:41:14: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:41:14: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:41:14: #1 total tags in treatment: 13200513 INFO @ Tue, 02 Aug 2022 10:41:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:41:14: #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 10:41:14: #1 tags after filtering in treatment: 13200513 INFO @ Tue, 02 Aug 2022 10:41:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:41:14: #1 finished! INFO @ Tue, 02 Aug 2022 10:41:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:41:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:41:15: #2 number of paired peaks: 301 WARNING @ Tue, 02 Aug 2022 10:41:15: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Tue, 02 Aug 2022 10:41:15: start model_add_line... INFO @ Tue, 02 Aug 2022 10:41:15: start X-correlation... INFO @ Tue, 02 Aug 2022 10:41:15: end of X-cor INFO @ Tue, 02 Aug 2022 10:41:15: #2 finished! INFO @ Tue, 02 Aug 2022 10:41:15: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:41:15: #2 alternative fragment length(s) may be 4,70 bps INFO @ Tue, 02 Aug 2022 10:41:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.20_model.r WARNING @ Tue, 02 Aug 2022 10:41:15: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:41:15: #2 You may need to consider one of the other alternative d(s): 4,70 WARNING @ Tue, 02 Aug 2022 10:41:15: #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 10:41:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:41:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:41:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:41:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:41:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:41:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435545/SRX10435545.20_summits.bed INFO @ Tue, 02 Aug 2022 10:41:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 3 millis CompletedMACS2peakCalling