Job ID = 16433323 SRX = SRX15407771 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: 00:03:55 10957458 reads; of these: 10957458 (100.00%) were unpaired; of these: 513717 (4.69%) aligned 0 times 8900524 (81.23%) aligned exactly 1 time 1543217 (14.08%) aligned >1 times 95.31% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 1349567 / 10443741 = 0.1292 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 09:45:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.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 09:45:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:45:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:45:11: 1000000 INFO @ Tue, 02 Aug 2022 09:45:18: 2000000 INFO @ Tue, 02 Aug 2022 09:45:23: 3000000 INFO @ Tue, 02 Aug 2022 09:45:29: 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 09:45:35: 5000000 INFO @ Tue, 02 Aug 2022 09:45:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.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 09:45:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:45:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:45:42: 6000000 INFO @ Tue, 02 Aug 2022 09:45:43: 1000000 INFO @ Tue, 02 Aug 2022 09:45:49: 7000000 INFO @ Tue, 02 Aug 2022 09:45:50: 2000000 INFO @ Tue, 02 Aug 2022 09:45:56: 8000000 INFO @ Tue, 02 Aug 2022 09:45:58: 3000000 INFO @ Tue, 02 Aug 2022 09:46:03: 9000000 BedGraph に変換中... INFO @ Tue, 02 Aug 2022 09:46:04: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:46:04: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:46:04: #1 total tags in treatment: 9094174 INFO @ Tue, 02 Aug 2022 09:46:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:46:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 09:46:04: #1 tags after filtering in treatment: 9094174 INFO @ Tue, 02 Aug 2022 09:46:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:46:04: #1 finished! INFO @ Tue, 02 Aug 2022 09:46:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:46:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:46:04: #2 number of paired peaks: 261 WARNING @ Tue, 02 Aug 2022 09:46:04: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Tue, 02 Aug 2022 09:46:04: start model_add_line... INFO @ Tue, 02 Aug 2022 09:46:04: start X-correlation... INFO @ Tue, 02 Aug 2022 09:46:04: end of X-cor INFO @ Tue, 02 Aug 2022 09:46:04: #2 finished! INFO @ Tue, 02 Aug 2022 09:46:04: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 09:46:04: #2 alternative fragment length(s) may be 4,74,547 bps INFO @ Tue, 02 Aug 2022 09:46:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.05_model.r WARNING @ Tue, 02 Aug 2022 09:46:04: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:46:04: #2 You may need to consider one of the other alternative d(s): 4,74,547 WARNING @ Tue, 02 Aug 2022 09:46:04: #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 09:46:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:46:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:46:05: 4000000 INFO @ Tue, 02 Aug 2022 09:46:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.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 09:46:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:46:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:46:11: 5000000 INFO @ Tue, 02 Aug 2022 09:46:13: 1000000 INFO @ Tue, 02 Aug 2022 09:46:18: 6000000 INFO @ Tue, 02 Aug 2022 09:46:21: 2000000 INFO @ Tue, 02 Aug 2022 09:46:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:46:25: 7000000 INFO @ Tue, 02 Aug 2022 09:46:29: 3000000 INFO @ Tue, 02 Aug 2022 09:46:32: 8000000 INFO @ Tue, 02 Aug 2022 09:46:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:46:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:46:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.05_summits.bed INFO @ Tue, 02 Aug 2022 09:46:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (769 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:46:36: 4000000 INFO @ Tue, 02 Aug 2022 09:46:39: 9000000 INFO @ Tue, 02 Aug 2022 09:46:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:46:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:46:39: #1 total tags in treatment: 9094174 INFO @ Tue, 02 Aug 2022 09:46:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:46:39: #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 09:46:39: #1 tags after filtering in treatment: 9094174 INFO @ Tue, 02 Aug 2022 09:46:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:46:39: #1 finished! INFO @ Tue, 02 Aug 2022 09:46:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:46:40: #2 number of paired peaks: 261 WARNING @ Tue, 02 Aug 2022 09:46:40: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Tue, 02 Aug 2022 09:46:40: start model_add_line... INFO @ Tue, 02 Aug 2022 09:46:40: start X-correlation... INFO @ Tue, 02 Aug 2022 09:46:40: end of X-cor INFO @ Tue, 02 Aug 2022 09:46:40: #2 finished! INFO @ Tue, 02 Aug 2022 09:46:40: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 09:46:40: #2 alternative fragment length(s) may be 4,74,547 bps INFO @ Tue, 02 Aug 2022 09:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.10_model.r WARNING @ Tue, 02 Aug 2022 09:46:40: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:46:40: #2 You may need to consider one of the other alternative d(s): 4,74,547 WARNING @ Tue, 02 Aug 2022 09:46:40: #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 09:46:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:46:44: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:46:51: 6000000 INFO @ Tue, 02 Aug 2022 09:46:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:46:57: 7000000 INFO @ Tue, 02 Aug 2022 09:47:04: 8000000 INFO @ Tue, 02 Aug 2022 09:47:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:47:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:47:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.10_summits.bed INFO @ Tue, 02 Aug 2022 09:47:06: Done! pass1 - making usageList (6 chroms): 1 millis BigWig に変換しました。 pass2 - checking and writing primary data (393 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:47:11: 9000000 INFO @ Tue, 02 Aug 2022 09:47:11: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:47:11: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:47:11: #1 total tags in treatment: 9094174 INFO @ Tue, 02 Aug 2022 09:47:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:47:11: #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 09:47:11: #1 tags after filtering in treatment: 9094174 INFO @ Tue, 02 Aug 2022 09:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:47:11: #1 finished! INFO @ Tue, 02 Aug 2022 09:47:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:47:12: #2 number of paired peaks: 261 WARNING @ Tue, 02 Aug 2022 09:47:12: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Tue, 02 Aug 2022 09:47:12: start model_add_line... INFO @ Tue, 02 Aug 2022 09:47:12: start X-correlation... INFO @ Tue, 02 Aug 2022 09:47:12: end of X-cor INFO @ Tue, 02 Aug 2022 09:47:12: #2 finished! INFO @ Tue, 02 Aug 2022 09:47:12: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 09:47:12: #2 alternative fragment length(s) may be 4,74,547 bps INFO @ Tue, 02 Aug 2022 09:47:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.20_model.r WARNING @ Tue, 02 Aug 2022 09:47:12: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:47:12: #2 You may need to consider one of the other alternative d(s): 4,74,547 WARNING @ Tue, 02 Aug 2022 09:47:12: #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 09:47:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:47:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407771/SRX15407771.20_summits.bed INFO @ Tue, 02 Aug 2022 09:47:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 19 millis CompletedMACS2peakCalling