Job ID = 16433882 SRX = SRX10274855 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: 00:06:54 18737772 reads; of these: 18737772 (100.00%) were unpaired; of these: 2137199 (11.41%) aligned 0 times 13626862 (72.72%) aligned exactly 1 time 2973711 (15.87%) aligned >1 times 88.59% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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] 2235654 / 16600573 = 0.1347 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 09:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.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 09:57:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:57:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:58:01: 1000000 INFO @ Tue, 02 Aug 2022 09:58:10: 2000000 INFO @ Tue, 02 Aug 2022 09:58:19: 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 09:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.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 09:58:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:58:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:58:28: 4000000 INFO @ Tue, 02 Aug 2022 09:58:30: 1000000 INFO @ Tue, 02 Aug 2022 09:58:37: 5000000 INFO @ Tue, 02 Aug 2022 09:58:38: 2000000 INFO @ Tue, 02 Aug 2022 09:58:45: 3000000 INFO @ Tue, 02 Aug 2022 09:58:46: 6000000 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 09:58:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.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 09:58:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:58:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:58:52: 4000000 INFO @ Tue, 02 Aug 2022 09:58:55: 7000000 INFO @ Tue, 02 Aug 2022 09:59:00: 5000000 INFO @ Tue, 02 Aug 2022 09:59:01: 1000000 INFO @ Tue, 02 Aug 2022 09:59:05: 8000000 INFO @ Tue, 02 Aug 2022 09:59:07: 6000000 INFO @ Tue, 02 Aug 2022 09:59:10: 2000000 INFO @ Tue, 02 Aug 2022 09:59:13: 7000000 INFO @ Tue, 02 Aug 2022 09:59:14: 9000000 INFO @ Tue, 02 Aug 2022 09:59:20: 3000000 INFO @ Tue, 02 Aug 2022 09:59:20: 8000000 INFO @ Tue, 02 Aug 2022 09:59:24: 10000000 INFO @ Tue, 02 Aug 2022 09:59:27: 9000000 INFO @ Tue, 02 Aug 2022 09:59:29: 4000000 INFO @ Tue, 02 Aug 2022 09:59:34: 11000000 INFO @ Tue, 02 Aug 2022 09:59:34: 10000000 INFO @ Tue, 02 Aug 2022 09:59:39: 5000000 INFO @ Tue, 02 Aug 2022 09:59:41: 11000000 INFO @ Tue, 02 Aug 2022 09:59:43: 12000000 INFO @ Tue, 02 Aug 2022 09:59:48: 12000000 INFO @ Tue, 02 Aug 2022 09:59:48: 6000000 INFO @ Tue, 02 Aug 2022 09:59:53: 13000000 INFO @ Tue, 02 Aug 2022 09:59:54: 13000000 INFO @ Tue, 02 Aug 2022 09:59:57: 7000000 INFO @ Tue, 02 Aug 2022 10:00:02: 14000000 INFO @ Tue, 02 Aug 2022 10:00:02: 14000000 INFO @ Tue, 02 Aug 2022 10:00:04: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:00:04: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:00:04: #1 total tags in treatment: 14364919 INFO @ Tue, 02 Aug 2022 10:00:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:00:04: #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 10:00:04: #1 tags after filtering in treatment: 14364919 INFO @ Tue, 02 Aug 2022 10:00:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:00:04: #1 finished! INFO @ Tue, 02 Aug 2022 10:00:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:00:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:00:05: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:00:05: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:00:05: #1 total tags in treatment: 14364919 INFO @ Tue, 02 Aug 2022 10:00:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:00:05: #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 10:00:05: #2 number of paired peaks: 288 WARNING @ Tue, 02 Aug 2022 10:00:05: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 02 Aug 2022 10:00:05: start model_add_line... INFO @ Tue, 02 Aug 2022 10:00:05: #1 tags after filtering in treatment: 14364919 INFO @ Tue, 02 Aug 2022 10:00:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:00:05: #1 finished! INFO @ Tue, 02 Aug 2022 10:00:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:00:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:00:05: start X-correlation... INFO @ Tue, 02 Aug 2022 10:00:06: end of X-cor INFO @ Tue, 02 Aug 2022 10:00:06: #2 finished! INFO @ Tue, 02 Aug 2022 10:00:06: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:00:06: #2 alternative fragment length(s) may be 3,74 bps INFO @ Tue, 02 Aug 2022 10:00:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.10_model.r WARNING @ Tue, 02 Aug 2022 10:00:06: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:00:06: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Tue, 02 Aug 2022 10:00:06: #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 10:00:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:00:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:00:06: #2 number of paired peaks: 288 WARNING @ Tue, 02 Aug 2022 10:00:06: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 02 Aug 2022 10:00:06: start model_add_line... INFO @ Tue, 02 Aug 2022 10:00:06: 8000000 INFO @ Tue, 02 Aug 2022 10:00:06: start X-correlation... INFO @ Tue, 02 Aug 2022 10:00:06: end of X-cor INFO @ Tue, 02 Aug 2022 10:00:06: #2 finished! INFO @ Tue, 02 Aug 2022 10:00:06: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:00:06: #2 alternative fragment length(s) may be 3,74 bps INFO @ Tue, 02 Aug 2022 10:00:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.05_model.r WARNING @ Tue, 02 Aug 2022 10:00:07: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:00:07: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Tue, 02 Aug 2022 10:00:07: #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 10:00:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:00:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:00:16: 9000000 INFO @ Tue, 02 Aug 2022 10:00:25: 10000000 INFO @ Tue, 02 Aug 2022 10:00:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:00:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:00:34: 11000000 INFO @ Tue, 02 Aug 2022 10:00:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:00:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:00:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.10_summits.bed INFO @ Tue, 02 Aug 2022 10:00:43: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (456 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:00:44: 12000000 INFO @ Tue, 02 Aug 2022 10:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.05_summits.bed INFO @ Tue, 02 Aug 2022 10:00:46: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (919 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:00:53: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:01:01: 14000000 INFO @ Tue, 02 Aug 2022 10:01:04: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:01:04: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:01:04: #1 total tags in treatment: 14364919 INFO @ Tue, 02 Aug 2022 10:01:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:01:04: #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 10:01:05: #1 tags after filtering in treatment: 14364919 INFO @ Tue, 02 Aug 2022 10:01:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:01:05: #1 finished! INFO @ Tue, 02 Aug 2022 10:01:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:01:06: #2 number of paired peaks: 288 WARNING @ Tue, 02 Aug 2022 10:01:06: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 02 Aug 2022 10:01:06: start model_add_line... INFO @ Tue, 02 Aug 2022 10:01:06: start X-correlation... INFO @ Tue, 02 Aug 2022 10:01:06: end of X-cor INFO @ Tue, 02 Aug 2022 10:01:06: #2 finished! INFO @ Tue, 02 Aug 2022 10:01:06: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:01:06: #2 alternative fragment length(s) may be 3,74 bps INFO @ Tue, 02 Aug 2022 10:01:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.20_model.r WARNING @ Tue, 02 Aug 2022 10:01:06: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:01:06: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Tue, 02 Aug 2022 10:01:06: #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 10:01:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:01:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:01:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10274855/SRX10274855.20_summits.bed INFO @ Tue, 02 Aug 2022 10:01:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (222 records, 4 fields): 13 millis CompletedMACS2peakCalling