Job ID = 16435140 SRX = SRX10435542 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: 00:05:16 16476072 reads; of these: 16476072 (100.00%) were unpaired; of these: 308288 (1.87%) aligned 0 times 13330568 (80.91%) aligned exactly 1 time 2837216 (17.22%) aligned >1 times 98.13% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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] 1739829 / 16167784 = 0.1076 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 10:47:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.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 10:47:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:47:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:47:09: 1000000 INFO @ Tue, 02 Aug 2022 10:47:15: 2000000 INFO @ Tue, 02 Aug 2022 10:47:21: 3000000 INFO @ Tue, 02 Aug 2022 10:47:27: 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 10:47:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.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 10:47:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:47:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:47:33: 5000000 INFO @ Tue, 02 Aug 2022 10:47:41: 6000000 INFO @ Tue, 02 Aug 2022 10:47:41: 1000000 INFO @ Tue, 02 Aug 2022 10:47:48: 7000000 INFO @ Tue, 02 Aug 2022 10:47:50: 2000000 INFO @ Tue, 02 Aug 2022 10:47:56: 8000000 INFO @ Tue, 02 Aug 2022 10:47:58: 3000000 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 10:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.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 10:48:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:48:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:48:04: 9000000 INFO @ Tue, 02 Aug 2022 10:48:07: 4000000 INFO @ Tue, 02 Aug 2022 10:48:11: 1000000 INFO @ Tue, 02 Aug 2022 10:48:12: 10000000 INFO @ Tue, 02 Aug 2022 10:48:15: 5000000 INFO @ Tue, 02 Aug 2022 10:48:19: 2000000 INFO @ Tue, 02 Aug 2022 10:48:20: 11000000 INFO @ Tue, 02 Aug 2022 10:48:23: 6000000 INFO @ Tue, 02 Aug 2022 10:48:27: 3000000 INFO @ Tue, 02 Aug 2022 10:48:28: 12000000 INFO @ Tue, 02 Aug 2022 10:48:31: 7000000 INFO @ Tue, 02 Aug 2022 10:48:35: 4000000 INFO @ Tue, 02 Aug 2022 10:48:35: 13000000 INFO @ Tue, 02 Aug 2022 10:48:40: 8000000 INFO @ Tue, 02 Aug 2022 10:48:43: 5000000 INFO @ Tue, 02 Aug 2022 10:48:43: 14000000 INFO @ Tue, 02 Aug 2022 10:48:47: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:48:47: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:48:47: #1 total tags in treatment: 14427955 INFO @ Tue, 02 Aug 2022 10:48:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:48:47: #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 10:48:47: #1 tags after filtering in treatment: 14427955 INFO @ Tue, 02 Aug 2022 10:48:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:48:47: #1 finished! INFO @ Tue, 02 Aug 2022 10:48:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:48:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:48:48: #2 number of paired peaks: 278 WARNING @ Tue, 02 Aug 2022 10:48:48: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 02 Aug 2022 10:48:48: start model_add_line... INFO @ Tue, 02 Aug 2022 10:48:48: start X-correlation... INFO @ Tue, 02 Aug 2022 10:48:48: 9000000 INFO @ Tue, 02 Aug 2022 10:48:48: end of X-cor INFO @ Tue, 02 Aug 2022 10:48:48: #2 finished! INFO @ Tue, 02 Aug 2022 10:48:48: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:48:48: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:48:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.05_model.r WARNING @ Tue, 02 Aug 2022 10:48:48: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:48:48: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:48:48: #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 10:48:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:48:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:48:50: 6000000 INFO @ Tue, 02 Aug 2022 10:48:56: 10000000 INFO @ Tue, 02 Aug 2022 10:48:58: 7000000 INFO @ Tue, 02 Aug 2022 10:49:04: 11000000 INFO @ Tue, 02 Aug 2022 10:49:06: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:49:12: 12000000 INFO @ Tue, 02 Aug 2022 10:49:14: 9000000 INFO @ Tue, 02 Aug 2022 10:49:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:49:20: 13000000 INFO @ Tue, 02 Aug 2022 10:49:22: 10000000 INFO @ Tue, 02 Aug 2022 10:49:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.05_summits.bed INFO @ Tue, 02 Aug 2022 10:49:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (949 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:49:28: 14000000 INFO @ Tue, 02 Aug 2022 10:49:30: 11000000 INFO @ Tue, 02 Aug 2022 10:49:31: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:49:31: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:49:31: #1 total tags in treatment: 14427955 INFO @ Tue, 02 Aug 2022 10:49:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:49:31: #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 10:49:32: #1 tags after filtering in treatment: 14427955 INFO @ Tue, 02 Aug 2022 10:49:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:49:32: #1 finished! INFO @ Tue, 02 Aug 2022 10:49:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:49:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:49:33: #2 number of paired peaks: 278 WARNING @ Tue, 02 Aug 2022 10:49:33: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 02 Aug 2022 10:49:33: start model_add_line... INFO @ Tue, 02 Aug 2022 10:49:33: start X-correlation... INFO @ Tue, 02 Aug 2022 10:49:33: end of X-cor INFO @ Tue, 02 Aug 2022 10:49:33: #2 finished! INFO @ Tue, 02 Aug 2022 10:49:33: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:49:33: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.10_model.r WARNING @ Tue, 02 Aug 2022 10:49:33: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:49:33: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:49:33: #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 10:49:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:49:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:49:36: 12000000 INFO @ Tue, 02 Aug 2022 10:49:43: 13000000 INFO @ Tue, 02 Aug 2022 10:49:49: 14000000 INFO @ Tue, 02 Aug 2022 10:49:52: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:49:52: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:49:52: #1 total tags in treatment: 14427955 INFO @ Tue, 02 Aug 2022 10:49:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:49:52: #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 10:49:52: #1 tags after filtering in treatment: 14427955 INFO @ Tue, 02 Aug 2022 10:49:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:49:52: #1 finished! INFO @ Tue, 02 Aug 2022 10:49:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:49:53: #2 number of paired peaks: 278 WARNING @ Tue, 02 Aug 2022 10:49:53: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 02 Aug 2022 10:49:53: start model_add_line... INFO @ Tue, 02 Aug 2022 10:49:53: start X-correlation... INFO @ Tue, 02 Aug 2022 10:49:53: end of X-cor INFO @ Tue, 02 Aug 2022 10:49:53: #2 finished! INFO @ Tue, 02 Aug 2022 10:49:53: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:49:53: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:49:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.20_model.r WARNING @ Tue, 02 Aug 2022 10:49:53: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:49:53: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:49:53: #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 10:49:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:49:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:49:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.10_summits.bed INFO @ Tue, 02 Aug 2022 10:50:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (488 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:50:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:50:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435542/SRX10435542.20_summits.bed INFO @ Tue, 02 Aug 2022 10:50:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (236 records, 4 fields): 14 millis CompletedMACS2peakCalling