Job ID = 16435013 SRX = SRX10435537 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:44 9949032 reads; of these: 9949032 (100.00%) were unpaired; of these: 826853 (8.31%) aligned 0 times 7627786 (76.67%) aligned exactly 1 time 1494393 (15.02%) aligned >1 times 91.69% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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_rmdupse_core] 915073 / 9122179 = 0.1003 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 10:39:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.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 10:39:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:39:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:39:18: 1000000 INFO @ Tue, 02 Aug 2022 10:39:27: 2000000 INFO @ Tue, 02 Aug 2022 10:39:35: 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 10:39:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.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 10:39:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:39:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:39:42: 4000000 INFO @ Tue, 02 Aug 2022 10:39:46: 1000000 INFO @ Tue, 02 Aug 2022 10:39:51: 5000000 INFO @ Tue, 02 Aug 2022 10:39:53: 2000000 INFO @ Tue, 02 Aug 2022 10:40:00: 3000000 INFO @ Tue, 02 Aug 2022 10:40:00: 6000000 INFO @ Tue, 02 Aug 2022 10:40:06: 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 10:40:08: 7000000 INFO @ Tue, 02 Aug 2022 10:40:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.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 10:40:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:40:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:40:13: 5000000 INFO @ Tue, 02 Aug 2022 10:40:15: 8000000 INFO @ Tue, 02 Aug 2022 10:40:17: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:40:17: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:40:17: #1 total tags in treatment: 8207106 INFO @ Tue, 02 Aug 2022 10:40:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:40:17: #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 10:40:17: #1 tags after filtering in treatment: 8207106 INFO @ Tue, 02 Aug 2022 10:40:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:40:17: #1 finished! INFO @ Tue, 02 Aug 2022 10:40:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:40:18: #2 number of paired peaks: 694 WARNING @ Tue, 02 Aug 2022 10:40:18: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 02 Aug 2022 10:40:18: start model_add_line... INFO @ Tue, 02 Aug 2022 10:40:18: 1000000 INFO @ Tue, 02 Aug 2022 10:40:18: start X-correlation... INFO @ Tue, 02 Aug 2022 10:40:18: end of X-cor INFO @ Tue, 02 Aug 2022 10:40:18: #2 finished! INFO @ Tue, 02 Aug 2022 10:40:18: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 10:40:18: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 02 Aug 2022 10:40:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.05_model.r WARNING @ Tue, 02 Aug 2022 10:40:18: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:40:18: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 02 Aug 2022 10:40:18: #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 10:40:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:40:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:40:20: 6000000 INFO @ Tue, 02 Aug 2022 10:40:27: 7000000 INFO @ Tue, 02 Aug 2022 10:40:27: 2000000 INFO @ Tue, 02 Aug 2022 10:40:34: 8000000 INFO @ Tue, 02 Aug 2022 10:40:35: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:40:35: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:40:35: #1 total tags in treatment: 8207106 INFO @ Tue, 02 Aug 2022 10:40:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:40:35: #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 10:40:35: #1 tags after filtering in treatment: 8207106 INFO @ Tue, 02 Aug 2022 10:40:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:40:35: #1 finished! INFO @ Tue, 02 Aug 2022 10:40:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:40:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:40:35: 3000000 INFO @ Tue, 02 Aug 2022 10:40:36: #2 number of paired peaks: 694 WARNING @ Tue, 02 Aug 2022 10:40:36: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 02 Aug 2022 10:40:36: start model_add_line... INFO @ Tue, 02 Aug 2022 10:40:36: start X-correlation... INFO @ Tue, 02 Aug 2022 10:40:36: end of X-cor INFO @ Tue, 02 Aug 2022 10:40:36: #2 finished! INFO @ Tue, 02 Aug 2022 10:40:36: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 10:40:36: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 02 Aug 2022 10:40:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.10_model.r WARNING @ Tue, 02 Aug 2022 10:40:36: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:40:36: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 02 Aug 2022 10:40:36: #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 10:40:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:40:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:40:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:40:43: 4000000 INFO @ Tue, 02 Aug 2022 10:40:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:40:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:40:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.05_summits.bed INFO @ Tue, 02 Aug 2022 10:40:47: Done! pass1 - making usageList (7 chroms): 15 millis pass2 - checking and writing primary data (2325 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:40:51: 5000000 INFO @ Tue, 02 Aug 2022 10:40:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:40:59: 6000000 INFO @ Tue, 02 Aug 2022 10:41:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:41:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:41:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.10_summits.bed INFO @ Tue, 02 Aug 2022 10:41:02: Done! pass1 - making usageList (7 chroms): 11 millis pass2 - checking and writing primary data (1416 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:41:07: 7000000 INFO @ Tue, 02 Aug 2022 10:41:15: 8000000 INFO @ Tue, 02 Aug 2022 10:41:17: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:41:17: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:41:17: #1 total tags in treatment: 8207106 INFO @ Tue, 02 Aug 2022 10:41:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:41:17: #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 10:41:17: #1 tags after filtering in treatment: 8207106 INFO @ Tue, 02 Aug 2022 10:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:41:17: #1 finished! INFO @ Tue, 02 Aug 2022 10:41:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:41:18: #2 number of paired peaks: 694 WARNING @ Tue, 02 Aug 2022 10:41:18: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 02 Aug 2022 10:41:18: start model_add_line... INFO @ Tue, 02 Aug 2022 10:41:18: start X-correlation... INFO @ Tue, 02 Aug 2022 10:41:18: end of X-cor INFO @ Tue, 02 Aug 2022 10:41:18: #2 finished! INFO @ Tue, 02 Aug 2022 10:41:18: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 10:41:18: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 02 Aug 2022 10:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.20_model.r WARNING @ Tue, 02 Aug 2022 10:41:18: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:41:18: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 02 Aug 2022 10:41:18: #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 10:41:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:41:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:41:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:41:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:41:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:41:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435537/SRX10435537.20_summits.bed INFO @ Tue, 02 Aug 2022 10:41:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (811 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。