Job ID = 14160855 SRX = SRX10569201 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: 00:06:55 22353040 reads; of these: 22353040 (100.00%) were unpaired; of these: 7259300 (32.48%) aligned 0 times 12577486 (56.27%) aligned exactly 1 time 2516254 (11.26%) aligned >1 times 67.52% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 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] 1916812 / 15093740 = 0.1270 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:47:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.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 @ Thu, 09 Dec 2021 04:47:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:47:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:47:21: 1000000 INFO @ Thu, 09 Dec 2021 04:47:26: 2000000 INFO @ Thu, 09 Dec 2021 04:47:32: 3000000 INFO @ Thu, 09 Dec 2021 04:47:37: 4000000 INFO @ Thu, 09 Dec 2021 04:47:43: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:47:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.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 @ Thu, 09 Dec 2021 04:47:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:47:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:47:48: 6000000 INFO @ Thu, 09 Dec 2021 04:47:51: 1000000 INFO @ Thu, 09 Dec 2021 04:47:54: 7000000 INFO @ Thu, 09 Dec 2021 04:47:57: 2000000 INFO @ Thu, 09 Dec 2021 04:48:00: 8000000 INFO @ Thu, 09 Dec 2021 04:48:03: 3000000 INFO @ Thu, 09 Dec 2021 04:48:05: 9000000 INFO @ Thu, 09 Dec 2021 04:48:09: 4000000 INFO @ Thu, 09 Dec 2021 04:48:11: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:48:15: 5000000 INFO @ Thu, 09 Dec 2021 04:48:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.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 @ Thu, 09 Dec 2021 04:48:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:48:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:48:17: 11000000 INFO @ Thu, 09 Dec 2021 04:48:21: 6000000 INFO @ Thu, 09 Dec 2021 04:48:21: 1000000 INFO @ Thu, 09 Dec 2021 04:48:23: 12000000 INFO @ Thu, 09 Dec 2021 04:48:27: 7000000 INFO @ Thu, 09 Dec 2021 04:48:27: 2000000 INFO @ Thu, 09 Dec 2021 04:48:29: 13000000 INFO @ Thu, 09 Dec 2021 04:48:30: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:48:30: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:48:30: #1 total tags in treatment: 13176928 INFO @ Thu, 09 Dec 2021 04:48:30: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:48:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:48:30: #1 tags after filtering in treatment: 13176928 INFO @ Thu, 09 Dec 2021 04:48:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:48:30: #1 finished! INFO @ Thu, 09 Dec 2021 04:48:30: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:48:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:48:31: #2 number of paired peaks: 234 WARNING @ Thu, 09 Dec 2021 04:48:31: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Thu, 09 Dec 2021 04:48:31: start model_add_line... INFO @ Thu, 09 Dec 2021 04:48:31: start X-correlation... INFO @ Thu, 09 Dec 2021 04:48:31: end of X-cor INFO @ Thu, 09 Dec 2021 04:48:31: #2 finished! INFO @ Thu, 09 Dec 2021 04:48:31: #2 predicted fragment length is 60 bps INFO @ Thu, 09 Dec 2021 04:48:31: #2 alternative fragment length(s) may be 2,60,585 bps INFO @ Thu, 09 Dec 2021 04:48:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.05_model.r WARNING @ Thu, 09 Dec 2021 04:48:31: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:48:31: #2 You may need to consider one of the other alternative d(s): 2,60,585 WARNING @ Thu, 09 Dec 2021 04:48:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:48:31: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:48:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:48:33: 8000000 INFO @ Thu, 09 Dec 2021 04:48:33: 3000000 INFO @ Thu, 09 Dec 2021 04:48:38: 9000000 INFO @ Thu, 09 Dec 2021 04:48:39: 4000000 INFO @ Thu, 09 Dec 2021 04:48:44: 10000000 INFO @ Thu, 09 Dec 2021 04:48:45: 5000000 INFO @ Thu, 09 Dec 2021 04:48:50: 11000000 INFO @ Thu, 09 Dec 2021 04:48:50: 6000000 INFO @ Thu, 09 Dec 2021 04:48:54: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:48:56: 12000000 INFO @ Thu, 09 Dec 2021 04:48:56: 7000000 INFO @ Thu, 09 Dec 2021 04:49:02: 13000000 INFO @ Thu, 09 Dec 2021 04:49:02: 8000000 INFO @ Thu, 09 Dec 2021 04:49:03: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:49:03: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:49:03: #1 total tags in treatment: 13176928 INFO @ Thu, 09 Dec 2021 04:49:03: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:49:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:49:03: #1 tags after filtering in treatment: 13176928 INFO @ Thu, 09 Dec 2021 04:49:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:49:03: #1 finished! INFO @ Thu, 09 Dec 2021 04:49:03: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:49:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:49:04: #2 number of paired peaks: 234 WARNING @ Thu, 09 Dec 2021 04:49:04: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Thu, 09 Dec 2021 04:49:04: start model_add_line... INFO @ Thu, 09 Dec 2021 04:49:04: start X-correlation... INFO @ Thu, 09 Dec 2021 04:49:04: end of X-cor INFO @ Thu, 09 Dec 2021 04:49:04: #2 finished! INFO @ Thu, 09 Dec 2021 04:49:04: #2 predicted fragment length is 60 bps INFO @ Thu, 09 Dec 2021 04:49:04: #2 alternative fragment length(s) may be 2,60,585 bps INFO @ Thu, 09 Dec 2021 04:49:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.10_model.r WARNING @ Thu, 09 Dec 2021 04:49:04: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:49:04: #2 You may need to consider one of the other alternative d(s): 2,60,585 WARNING @ Thu, 09 Dec 2021 04:49:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:49:04: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:49:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.05_summits.bed INFO @ Thu, 09 Dec 2021 04:49:05: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (509 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:49:08: 9000000 INFO @ Thu, 09 Dec 2021 04:49:13: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:49:19: 11000000 INFO @ Thu, 09 Dec 2021 04:49:24: 12000000 INFO @ Thu, 09 Dec 2021 04:49:28: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:49:30: 13000000 INFO @ Thu, 09 Dec 2021 04:49:31: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:49:31: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:49:31: #1 total tags in treatment: 13176928 INFO @ Thu, 09 Dec 2021 04:49:31: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:49:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:49:31: #1 tags after filtering in treatment: 13176928 INFO @ Thu, 09 Dec 2021 04:49:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:49:31: #1 finished! INFO @ Thu, 09 Dec 2021 04:49:31: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:49:32: #2 number of paired peaks: 234 WARNING @ Thu, 09 Dec 2021 04:49:32: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Thu, 09 Dec 2021 04:49:32: start model_add_line... INFO @ Thu, 09 Dec 2021 04:49:32: start X-correlation... INFO @ Thu, 09 Dec 2021 04:49:32: end of X-cor INFO @ Thu, 09 Dec 2021 04:49:32: #2 finished! INFO @ Thu, 09 Dec 2021 04:49:32: #2 predicted fragment length is 60 bps INFO @ Thu, 09 Dec 2021 04:49:32: #2 alternative fragment length(s) may be 2,60,585 bps INFO @ Thu, 09 Dec 2021 04:49:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.20_model.r WARNING @ Thu, 09 Dec 2021 04:49:32: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:49:32: #2 You may need to consider one of the other alternative d(s): 2,60,585 WARNING @ Thu, 09 Dec 2021 04:49:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:49:32: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:49:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:49:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:49:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:49:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.10_summits.bed INFO @ Thu, 09 Dec 2021 04:49:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (320 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:49:56: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:50:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:50:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:50:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569201/SRX10569201.20_summits.bed INFO @ Thu, 09 Dec 2021 04:50:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 1 millis CompletedMACS2peakCalling