Job ID = 16435144 SRX = SRX10435545 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:36 15285451 reads; of these: 15285451 (100.00%) were unpaired; of these: 556630 (3.64%) aligned 0 times 12182765 (79.70%) aligned exactly 1 time 2546056 (16.66%) aligned >1 times 96.36% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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] 1528227 / 14728821 = 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 10:46:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 10:46:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:46:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:46:45: 1000000 INFO @ Tue, 02 Aug 2022 10:46:50: 2000000 INFO @ Tue, 02 Aug 2022 10:46:56: 3000000 INFO @ Tue, 02 Aug 2022 10:47:01: 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 10:47:06: 5000000 INFO @ Tue, 02 Aug 2022 10:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 10:47:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:47:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:47:12: 6000000 INFO @ Tue, 02 Aug 2022 10:47:15: 1000000 INFO @ Tue, 02 Aug 2022 10:47:18: 7000000 INFO @ Tue, 02 Aug 2022 10:47:21: 2000000 INFO @ Tue, 02 Aug 2022 10:47:24: 8000000 INFO @ Tue, 02 Aug 2022 10:47:28: 3000000 INFO @ Tue, 02 Aug 2022 10:47:30: 9000000 INFO @ Tue, 02 Aug 2022 10:47:34: 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 10:47:36: 10000000 INFO @ Tue, 02 Aug 2022 10:47:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 10:47:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:47:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:47:40: 5000000 INFO @ Tue, 02 Aug 2022 10:47:42: 11000000 INFO @ Tue, 02 Aug 2022 10:47:44: 1000000 INFO @ Tue, 02 Aug 2022 10:47:46: 6000000 INFO @ Tue, 02 Aug 2022 10:47:48: 12000000 INFO @ Tue, 02 Aug 2022 10:47:50: 2000000 INFO @ Tue, 02 Aug 2022 10:47:53: 7000000 INFO @ Tue, 02 Aug 2022 10:47:54: 13000000 INFO @ Tue, 02 Aug 2022 10:47:56: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:47:56: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:47:56: #1 total tags in treatment: 13200594 INFO @ Tue, 02 Aug 2022 10:47:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:47:56: #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 10:47:56: #1 tags after filtering in treatment: 13200594 INFO @ Tue, 02 Aug 2022 10:47:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:47:56: #1 finished! INFO @ Tue, 02 Aug 2022 10:47:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:47:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:47:56: 3000000 INFO @ Tue, 02 Aug 2022 10:47:57: #2 number of paired peaks: 299 WARNING @ Tue, 02 Aug 2022 10:47:57: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Tue, 02 Aug 2022 10:47:57: start model_add_line... INFO @ Tue, 02 Aug 2022 10:47:57: start X-correlation... INFO @ Tue, 02 Aug 2022 10:47:57: end of X-cor INFO @ Tue, 02 Aug 2022 10:47:57: #2 finished! INFO @ Tue, 02 Aug 2022 10:47:57: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:47:57: #2 alternative fragment length(s) may be 3,70,577 bps INFO @ Tue, 02 Aug 2022 10:47:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.05_model.r WARNING @ Tue, 02 Aug 2022 10:47:57: #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 10:47:57: #2 You may need to consider one of the other alternative d(s): 3,70,577 WARNING @ Tue, 02 Aug 2022 10:47:57: #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 10:47:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:47:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:47:59: 8000000 INFO @ Tue, 02 Aug 2022 10:48:02: 4000000 INFO @ Tue, 02 Aug 2022 10:48:06: 9000000 INFO @ Tue, 02 Aug 2022 10:48:08: 5000000 INFO @ Tue, 02 Aug 2022 10:48:12: 10000000 INFO @ Tue, 02 Aug 2022 10:48:14: 6000000 INFO @ Tue, 02 Aug 2022 10:48:19: 11000000 INFO @ Tue, 02 Aug 2022 10:48:20: 7000000 INFO @ Tue, 02 Aug 2022 10:48:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:48:26: 12000000 INFO @ Tue, 02 Aug 2022 10:48:26: 8000000 INFO @ Tue, 02 Aug 2022 10:48:32: 9000000 INFO @ Tue, 02 Aug 2022 10:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:48:32: 13000000 INFO @ Tue, 02 Aug 2022 10:48:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:48:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.05_summits.bed INFO @ Tue, 02 Aug 2022 10:48:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (809 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:48:34: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:48:34: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:48:34: #1 total tags in treatment: 13200594 INFO @ Tue, 02 Aug 2022 10:48:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:48:34: #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 10:48:34: #1 tags after filtering in treatment: 13200594 INFO @ Tue, 02 Aug 2022 10:48:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:48:34: #1 finished! INFO @ Tue, 02 Aug 2022 10:48:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:48:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:48:35: #2 number of paired peaks: 299 WARNING @ Tue, 02 Aug 2022 10:48:35: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Tue, 02 Aug 2022 10:48:35: start model_add_line... INFO @ Tue, 02 Aug 2022 10:48:35: start X-correlation... INFO @ Tue, 02 Aug 2022 10:48:35: end of X-cor INFO @ Tue, 02 Aug 2022 10:48:35: #2 finished! INFO @ Tue, 02 Aug 2022 10:48:35: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:48:35: #2 alternative fragment length(s) may be 3,70,577 bps INFO @ Tue, 02 Aug 2022 10:48:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.10_model.r WARNING @ Tue, 02 Aug 2022 10:48:35: #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 10:48:35: #2 You may need to consider one of the other alternative d(s): 3,70,577 WARNING @ Tue, 02 Aug 2022 10:48:35: #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 10:48:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:48:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:48:38: 10000000 INFO @ Tue, 02 Aug 2022 10:48:44: 11000000 INFO @ Tue, 02 Aug 2022 10:48:49: 12000000 INFO @ Tue, 02 Aug 2022 10:48:54: 13000000 INFO @ Tue, 02 Aug 2022 10:48:56: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:48:56: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:48:56: #1 total tags in treatment: 13200594 INFO @ Tue, 02 Aug 2022 10:48:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:48:56: #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 10:48:56: #1 tags after filtering in treatment: 13200594 INFO @ Tue, 02 Aug 2022 10:48:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:48:56: #1 finished! INFO @ Tue, 02 Aug 2022 10:48:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:48:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:48:57: #2 number of paired peaks: 299 WARNING @ Tue, 02 Aug 2022 10:48:57: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Tue, 02 Aug 2022 10:48:57: start model_add_line... INFO @ Tue, 02 Aug 2022 10:48:57: start X-correlation... INFO @ Tue, 02 Aug 2022 10:48:57: end of X-cor INFO @ Tue, 02 Aug 2022 10:48:57: #2 finished! INFO @ Tue, 02 Aug 2022 10:48:57: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:48:57: #2 alternative fragment length(s) may be 3,70,577 bps INFO @ Tue, 02 Aug 2022 10:48:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.20_model.r WARNING @ Tue, 02 Aug 2022 10:48:57: #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 10:48:57: #2 You may need to consider one of the other alternative d(s): 3,70,577 WARNING @ Tue, 02 Aug 2022 10:48:57: #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 10:48:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:48:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:48:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:49:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:49:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:49:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.10_summits.bed INFO @ Tue, 02 Aug 2022 10:49:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (453 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:49:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:49:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:49:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:49:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435545/SRX10435545.20_summits.bed INFO @ Tue, 02 Aug 2022 10:49:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 18 millis CompletedMACS2peakCalling