Job ID = 16433870 SRX = SRX15407790 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: 00:05:32 17496603 reads; of these: 17496603 (100.00%) were unpaired; of these: 393734 (2.25%) aligned 0 times 14591237 (83.39%) aligned exactly 1 time 2511632 (14.35%) aligned >1 times 97.75% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 1703422 / 17102869 = 0.0996 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 09:55:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.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 09:55:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:55:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:55:23: 1000000 INFO @ Tue, 02 Aug 2022 09:55:29: 2000000 INFO @ Tue, 02 Aug 2022 09:55:35: 3000000 INFO @ Tue, 02 Aug 2022 09:55:41: 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 09:55:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.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 09:55:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:55:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:55:47: 5000000 INFO @ Tue, 02 Aug 2022 09:55:53: 1000000 INFO @ Tue, 02 Aug 2022 09:55:53: 6000000 INFO @ Tue, 02 Aug 2022 09:55:59: 2000000 INFO @ Tue, 02 Aug 2022 09:56:00: 7000000 INFO @ Tue, 02 Aug 2022 09:56:06: 3000000 INFO @ Tue, 02 Aug 2022 09:56:07: 8000000 INFO @ Tue, 02 Aug 2022 09:56:12: 4000000 INFO @ Tue, 02 Aug 2022 09:56:13: 9000000 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 09:56:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.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 09:56:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:56:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:56:19: 5000000 INFO @ Tue, 02 Aug 2022 09:56:20: 10000000 INFO @ Tue, 02 Aug 2022 09:56:23: 1000000 INFO @ Tue, 02 Aug 2022 09:56:26: 6000000 INFO @ Tue, 02 Aug 2022 09:56:27: 11000000 INFO @ Tue, 02 Aug 2022 09:56:30: 2000000 INFO @ Tue, 02 Aug 2022 09:56:33: 7000000 INFO @ Tue, 02 Aug 2022 09:56:34: 12000000 INFO @ Tue, 02 Aug 2022 09:56:37: 3000000 INFO @ Tue, 02 Aug 2022 09:56:40: 8000000 INFO @ Tue, 02 Aug 2022 09:56:41: 13000000 INFO @ Tue, 02 Aug 2022 09:56:44: 4000000 INFO @ Tue, 02 Aug 2022 09:56:47: 9000000 INFO @ Tue, 02 Aug 2022 09:56:47: 14000000 INFO @ Tue, 02 Aug 2022 09:56:51: 5000000 INFO @ Tue, 02 Aug 2022 09:56:53: 10000000 INFO @ Tue, 02 Aug 2022 09:56:54: 15000000 INFO @ Tue, 02 Aug 2022 09:56:57: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:56:57: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:56:57: #1 total tags in treatment: 15399447 INFO @ Tue, 02 Aug 2022 09:56:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:56:57: #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 09:56:57: #1 tags after filtering in treatment: 15399447 INFO @ Tue, 02 Aug 2022 09:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:56:57: #1 finished! INFO @ Tue, 02 Aug 2022 09:56:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:56:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:56:57: 6000000 INFO @ Tue, 02 Aug 2022 09:56:58: #2 number of paired peaks: 184 WARNING @ Tue, 02 Aug 2022 09:56:58: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 02 Aug 2022 09:56:58: start model_add_line... INFO @ Tue, 02 Aug 2022 09:56:58: start X-correlation... INFO @ Tue, 02 Aug 2022 09:56:58: end of X-cor INFO @ Tue, 02 Aug 2022 09:56:58: #2 finished! INFO @ Tue, 02 Aug 2022 09:56:58: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 09:56:58: #2 alternative fragment length(s) may be 2,71,596 bps INFO @ Tue, 02 Aug 2022 09:56:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.05_model.r WARNING @ Tue, 02 Aug 2022 09:56:58: #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 09:56:58: #2 You may need to consider one of the other alternative d(s): 2,71,596 WARNING @ Tue, 02 Aug 2022 09:56:58: #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 09:56:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:56:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:57:00: 11000000 INFO @ Tue, 02 Aug 2022 09:57:04: 7000000 INFO @ Tue, 02 Aug 2022 09:57:07: 12000000 INFO @ Tue, 02 Aug 2022 09:57:11: 8000000 INFO @ Tue, 02 Aug 2022 09:57:14: 13000000 INFO @ Tue, 02 Aug 2022 09:57:18: 9000000 INFO @ Tue, 02 Aug 2022 09:57:21: 14000000 INFO @ Tue, 02 Aug 2022 09:57:25: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:57:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:57:27: 15000000 INFO @ Tue, 02 Aug 2022 09:57:30: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:57:30: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:57:30: #1 total tags in treatment: 15399447 INFO @ Tue, 02 Aug 2022 09:57:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:57:30: #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 09:57:30: #1 tags after filtering in treatment: 15399447 INFO @ Tue, 02 Aug 2022 09:57:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:57:30: #1 finished! INFO @ Tue, 02 Aug 2022 09:57:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:57:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:57:31: #2 number of paired peaks: 184 WARNING @ Tue, 02 Aug 2022 09:57:31: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 02 Aug 2022 09:57:31: start model_add_line... INFO @ Tue, 02 Aug 2022 09:57:31: start X-correlation... INFO @ Tue, 02 Aug 2022 09:57:31: end of X-cor INFO @ Tue, 02 Aug 2022 09:57:31: #2 finished! INFO @ Tue, 02 Aug 2022 09:57:31: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 09:57:31: #2 alternative fragment length(s) may be 2,71,596 bps INFO @ Tue, 02 Aug 2022 09:57:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.10_model.r WARNING @ Tue, 02 Aug 2022 09:57:31: #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 09:57:31: #2 You may need to consider one of the other alternative d(s): 2,71,596 WARNING @ Tue, 02 Aug 2022 09:57:31: #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 09:57:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:57:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:57:32: 11000000 INFO @ Tue, 02 Aug 2022 09:57:38: 12000000 INFO @ Tue, 02 Aug 2022 09:57:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:57:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:57:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.05_summits.bed INFO @ Tue, 02 Aug 2022 09:57:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (560 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:57:44: 13000000 INFO @ Tue, 02 Aug 2022 09:57:50: 14000000 INFO @ Tue, 02 Aug 2022 09:57:57: 15000000 INFO @ Tue, 02 Aug 2022 09:57:59: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:57:59: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:57:59: #1 total tags in treatment: 15399447 INFO @ Tue, 02 Aug 2022 09:57:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:57:59: #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 09:57:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:57:59: #1 tags after filtering in treatment: 15399447 INFO @ Tue, 02 Aug 2022 09:57:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:57:59: #1 finished! INFO @ Tue, 02 Aug 2022 09:57:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:57:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:58:00: #2 number of paired peaks: 184 WARNING @ Tue, 02 Aug 2022 09:58:00: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 02 Aug 2022 09:58:00: start model_add_line... INFO @ Tue, 02 Aug 2022 09:58:00: start X-correlation... INFO @ Tue, 02 Aug 2022 09:58:00: end of X-cor INFO @ Tue, 02 Aug 2022 09:58:00: #2 finished! INFO @ Tue, 02 Aug 2022 09:58:00: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 09:58:00: #2 alternative fragment length(s) may be 2,71,596 bps INFO @ Tue, 02 Aug 2022 09:58:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.20_model.r WARNING @ Tue, 02 Aug 2022 09:58:00: #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 09:58:00: #2 You may need to consider one of the other alternative d(s): 2,71,596 WARNING @ Tue, 02 Aug 2022 09:58:00: #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 09:58:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:58:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:58:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:58:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:58:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.10_summits.bed INFO @ Tue, 02 Aug 2022 09:58:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (374 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:58:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:58:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:58:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:58:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407790/SRX15407790.20_summits.bed INFO @ Tue, 02 Aug 2022 09:58:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (195 records, 4 fields): 35 millis CompletedMACS2peakCalling