Job ID = 16434915 SRX = SRX10435521 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: 00:06:19 19602543 reads; of these: 19602543 (100.00%) were unpaired; of these: 1500528 (7.65%) aligned 0 times 15224546 (77.67%) aligned exactly 1 time 2877469 (14.68%) aligned >1 times 92.35% overall alignment rate Time searching: 00:06:19 Overall time: 00:06:19 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] 1992969 / 18102015 = 0.1101 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 10:25:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.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 10:25:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:25:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:25:14: 1000000 INFO @ Tue, 02 Aug 2022 10:25:21: 2000000 INFO @ Tue, 02 Aug 2022 10:25:28: 3000000 INFO @ Tue, 02 Aug 2022 10:25:34: 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 10:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.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 10:25:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:25:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:25:41: 5000000 INFO @ Tue, 02 Aug 2022 10:25:44: 1000000 INFO @ Tue, 02 Aug 2022 10:25:48: 6000000 INFO @ Tue, 02 Aug 2022 10:25:50: 2000000 INFO @ Tue, 02 Aug 2022 10:25:55: 7000000 INFO @ Tue, 02 Aug 2022 10:25:57: 3000000 INFO @ Tue, 02 Aug 2022 10:26:02: 8000000 INFO @ Tue, 02 Aug 2022 10:26:03: 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 10:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.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 10:26:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:26:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:26:09: 5000000 INFO @ Tue, 02 Aug 2022 10:26:09: 9000000 INFO @ Tue, 02 Aug 2022 10:26:14: 1000000 INFO @ Tue, 02 Aug 2022 10:26:16: 6000000 INFO @ Tue, 02 Aug 2022 10:26:16: 10000000 INFO @ Tue, 02 Aug 2022 10:26:20: 2000000 INFO @ Tue, 02 Aug 2022 10:26:22: 7000000 INFO @ Tue, 02 Aug 2022 10:26:24: 11000000 INFO @ Tue, 02 Aug 2022 10:26:26: 3000000 INFO @ Tue, 02 Aug 2022 10:26:28: 8000000 INFO @ Tue, 02 Aug 2022 10:26:31: 12000000 INFO @ Tue, 02 Aug 2022 10:26:33: 4000000 INFO @ Tue, 02 Aug 2022 10:26:35: 9000000 INFO @ Tue, 02 Aug 2022 10:26:38: 13000000 INFO @ Tue, 02 Aug 2022 10:26:39: 5000000 INFO @ Tue, 02 Aug 2022 10:26:41: 10000000 INFO @ Tue, 02 Aug 2022 10:26:45: 14000000 INFO @ Tue, 02 Aug 2022 10:26:45: 6000000 INFO @ Tue, 02 Aug 2022 10:26:47: 11000000 INFO @ Tue, 02 Aug 2022 10:26:52: 15000000 INFO @ Tue, 02 Aug 2022 10:26:52: 7000000 INFO @ Tue, 02 Aug 2022 10:26:54: 12000000 INFO @ Tue, 02 Aug 2022 10:26:58: 8000000 INFO @ Tue, 02 Aug 2022 10:26:58: 16000000 INFO @ Tue, 02 Aug 2022 10:26:59: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:26:59: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:26:59: #1 total tags in treatment: 16109046 INFO @ Tue, 02 Aug 2022 10:26:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:26:59: #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 10:26:59: #1 tags after filtering in treatment: 16109046 INFO @ Tue, 02 Aug 2022 10:26:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:26:59: #1 finished! INFO @ Tue, 02 Aug 2022 10:26:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:26:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:27:00: 13000000 INFO @ Tue, 02 Aug 2022 10:27:01: #2 number of paired peaks: 219 WARNING @ Tue, 02 Aug 2022 10:27:01: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 02 Aug 2022 10:27:01: start model_add_line... INFO @ Tue, 02 Aug 2022 10:27:01: start X-correlation... INFO @ Tue, 02 Aug 2022 10:27:01: end of X-cor INFO @ Tue, 02 Aug 2022 10:27:01: #2 finished! INFO @ Tue, 02 Aug 2022 10:27:01: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:27:01: #2 alternative fragment length(s) may be 3,64,71 bps INFO @ Tue, 02 Aug 2022 10:27:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.05_model.r WARNING @ Tue, 02 Aug 2022 10:27:01: #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 10:27:01: #2 You may need to consider one of the other alternative d(s): 3,64,71 WARNING @ Tue, 02 Aug 2022 10:27:01: #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 10:27:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:27:04: 9000000 INFO @ Tue, 02 Aug 2022 10:27:06: 14000000 INFO @ Tue, 02 Aug 2022 10:27:10: 10000000 INFO @ Tue, 02 Aug 2022 10:27:12: 15000000 INFO @ Tue, 02 Aug 2022 10:27:16: 11000000 INFO @ Tue, 02 Aug 2022 10:27:17: 16000000 INFO @ Tue, 02 Aug 2022 10:27:18: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:27:18: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:27:18: #1 total tags in treatment: 16109046 INFO @ Tue, 02 Aug 2022 10:27:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:27:18: #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 10:27:18: #1 tags after filtering in treatment: 16109046 INFO @ Tue, 02 Aug 2022 10:27:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:27:18: #1 finished! INFO @ Tue, 02 Aug 2022 10:27:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:27:18: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:27:19: #2 number of paired peaks: 219 WARNING @ Tue, 02 Aug 2022 10:27:19: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 02 Aug 2022 10:27:19: start model_add_line... INFO @ Tue, 02 Aug 2022 10:27:19: start X-correlation... INFO @ Tue, 02 Aug 2022 10:27:19: end of X-cor INFO @ Tue, 02 Aug 2022 10:27:19: #2 finished! INFO @ Tue, 02 Aug 2022 10:27:19: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:27:19: #2 alternative fragment length(s) may be 3,64,71 bps INFO @ Tue, 02 Aug 2022 10:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.10_model.r WARNING @ Tue, 02 Aug 2022 10:27:20: #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 10:27:20: #2 You may need to consider one of the other alternative d(s): 3,64,71 WARNING @ Tue, 02 Aug 2022 10:27:20: #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 10:27:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:27:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:27:21: 12000000 INFO @ Tue, 02 Aug 2022 10:27:27: 13000000 INFO @ Tue, 02 Aug 2022 10:27:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:27:32: 14000000 INFO @ Tue, 02 Aug 2022 10:27:38: 15000000 INFO @ Tue, 02 Aug 2022 10:27:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:27:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:27:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.05_summits.bed INFO @ Tue, 02 Aug 2022 10:27:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (655 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:27:43: 16000000 INFO @ Tue, 02 Aug 2022 10:27:44: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:27:44: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:27:44: #1 total tags in treatment: 16109046 INFO @ Tue, 02 Aug 2022 10:27:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:27:44: #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 10:27:44: #1 tags after filtering in treatment: 16109046 INFO @ Tue, 02 Aug 2022 10:27:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:27:44: #1 finished! INFO @ Tue, 02 Aug 2022 10:27:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:27:45: #2 number of paired peaks: 219 WARNING @ Tue, 02 Aug 2022 10:27:45: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 02 Aug 2022 10:27:45: start model_add_line... INFO @ Tue, 02 Aug 2022 10:27:45: start X-correlation... INFO @ Tue, 02 Aug 2022 10:27:45: end of X-cor INFO @ Tue, 02 Aug 2022 10:27:45: #2 finished! INFO @ Tue, 02 Aug 2022 10:27:45: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:27:45: #2 alternative fragment length(s) may be 3,64,71 bps INFO @ Tue, 02 Aug 2022 10:27:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.20_model.r WARNING @ Tue, 02 Aug 2022 10:27:45: #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 10:27:45: #2 You may need to consider one of the other alternative d(s): 3,64,71 WARNING @ Tue, 02 Aug 2022 10:27:45: #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 10:27:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:27:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:27:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:28:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:28:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:28:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.10_summits.bed INFO @ Tue, 02 Aug 2022 10:28:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (418 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:28:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:28:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:28:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:28:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435521/SRX10435521.20_summits.bed INFO @ Tue, 02 Aug 2022 10:28:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (226 records, 4 fields): 15 millis CompletedMACS2peakCalling