Job ID = 16432830 SRX = SRX10274854 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20026182 spots for SRR13895160/SRR13895160.sra Written 20026182 spots for SRR13895160/SRR13895160.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434147 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:32 20026182 reads; of these: 20026182 (100.00%) were unpaired; of these: 737625 (3.68%) aligned 0 times 15830508 (79.05%) aligned exactly 1 time 3458049 (17.27%) aligned >1 times 96.32% overall alignment rate Time searching: 00:09:32 Overall time: 00:09:32 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] 3528758 / 19288557 = 0.1829 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 09:49:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.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 09:49:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:49:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:49:53: 1000000 INFO @ Tue, 02 Aug 2022 09:50:03: 2000000 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 09:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.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 09:50:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:50:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:50:14: 3000000 INFO @ Tue, 02 Aug 2022 09:50:23: 1000000 INFO @ Tue, 02 Aug 2022 09:50:25: 4000000 INFO @ Tue, 02 Aug 2022 09:50:34: 2000000 INFO @ Tue, 02 Aug 2022 09:50:37: 5000000 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 09:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.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 09:50:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:50:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:50:46: 3000000 INFO @ Tue, 02 Aug 2022 09:50:48: 6000000 INFO @ Tue, 02 Aug 2022 09:50:57: 1000000 INFO @ Tue, 02 Aug 2022 09:50:58: 4000000 INFO @ Tue, 02 Aug 2022 09:51:00: 7000000 INFO @ Tue, 02 Aug 2022 09:51:08: 2000000 INFO @ Tue, 02 Aug 2022 09:51:10: 5000000 INFO @ Tue, 02 Aug 2022 09:51:11: 8000000 INFO @ Tue, 02 Aug 2022 09:51:21: 3000000 INFO @ Tue, 02 Aug 2022 09:51:22: 6000000 INFO @ Tue, 02 Aug 2022 09:51:23: 9000000 INFO @ Tue, 02 Aug 2022 09:51:32: 4000000 INFO @ Tue, 02 Aug 2022 09:51:35: 7000000 INFO @ Tue, 02 Aug 2022 09:51:35: 10000000 INFO @ Tue, 02 Aug 2022 09:51:44: 5000000 INFO @ Tue, 02 Aug 2022 09:51:46: 11000000 INFO @ Tue, 02 Aug 2022 09:51:47: 8000000 INFO @ Tue, 02 Aug 2022 09:51:56: 6000000 INFO @ Tue, 02 Aug 2022 09:51:57: 12000000 INFO @ Tue, 02 Aug 2022 09:52:00: 9000000 INFO @ Tue, 02 Aug 2022 09:52:07: 7000000 INFO @ Tue, 02 Aug 2022 09:52:08: 13000000 INFO @ Tue, 02 Aug 2022 09:52:13: 10000000 INFO @ Tue, 02 Aug 2022 09:52:18: 8000000 INFO @ Tue, 02 Aug 2022 09:52:20: 14000000 INFO @ Tue, 02 Aug 2022 09:52:25: 11000000 INFO @ Tue, 02 Aug 2022 09:52:29: 9000000 INFO @ Tue, 02 Aug 2022 09:52:31: 15000000 INFO @ Tue, 02 Aug 2022 09:52:38: 12000000 INFO @ Tue, 02 Aug 2022 09:52:39: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:52:39: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:52:39: #1 total tags in treatment: 15759799 INFO @ Tue, 02 Aug 2022 09:52:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:52:39: #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 09:52:40: #1 tags after filtering in treatment: 15759799 INFO @ Tue, 02 Aug 2022 09:52:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:52:40: #1 finished! INFO @ Tue, 02 Aug 2022 09:52:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:52:40: 10000000 INFO @ Tue, 02 Aug 2022 09:52:41: #2 number of paired peaks: 337 WARNING @ Tue, 02 Aug 2022 09:52:41: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Tue, 02 Aug 2022 09:52:41: start model_add_line... INFO @ Tue, 02 Aug 2022 09:52:41: start X-correlation... INFO @ Tue, 02 Aug 2022 09:52:41: end of X-cor INFO @ Tue, 02 Aug 2022 09:52:41: #2 finished! INFO @ Tue, 02 Aug 2022 09:52:41: #2 predicted fragment length is 107 bps INFO @ Tue, 02 Aug 2022 09:52:41: #2 alternative fragment length(s) may be 4,94,107 bps INFO @ Tue, 02 Aug 2022 09:52:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.05_model.r WARNING @ Tue, 02 Aug 2022 09:52:41: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:52:41: #2 You may need to consider one of the other alternative d(s): 4,94,107 WARNING @ Tue, 02 Aug 2022 09:52:41: #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 09:52:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:52:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:52:50: 13000000 INFO @ Tue, 02 Aug 2022 09:52:50: 11000000 INFO @ Tue, 02 Aug 2022 09:53:01: 12000000 INFO @ Tue, 02 Aug 2022 09:53:01: 14000000 INFO @ Tue, 02 Aug 2022 09:53:11: 13000000 INFO @ Tue, 02 Aug 2022 09:53:12: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:53:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:53:20: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:53:20: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:53:20: #1 total tags in treatment: 15759799 INFO @ Tue, 02 Aug 2022 09:53:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:53:20: #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 09:53:20: #1 tags after filtering in treatment: 15759799 INFO @ Tue, 02 Aug 2022 09:53:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:53:20: #1 finished! INFO @ Tue, 02 Aug 2022 09:53:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:53:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:53:21: 14000000 INFO @ Tue, 02 Aug 2022 09:53:21: #2 number of paired peaks: 337 WARNING @ Tue, 02 Aug 2022 09:53:21: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Tue, 02 Aug 2022 09:53:21: start model_add_line... INFO @ Tue, 02 Aug 2022 09:53:21: start X-correlation... INFO @ Tue, 02 Aug 2022 09:53:21: end of X-cor INFO @ Tue, 02 Aug 2022 09:53:21: #2 finished! INFO @ Tue, 02 Aug 2022 09:53:21: #2 predicted fragment length is 107 bps INFO @ Tue, 02 Aug 2022 09:53:21: #2 alternative fragment length(s) may be 4,94,107 bps INFO @ Tue, 02 Aug 2022 09:53:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.10_model.r WARNING @ Tue, 02 Aug 2022 09:53:21: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:53:21: #2 You may need to consider one of the other alternative d(s): 4,94,107 WARNING @ Tue, 02 Aug 2022 09:53:21: #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 09:53:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:53:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:53:30: 15000000 INFO @ Tue, 02 Aug 2022 09:53:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:53:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:53:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.05_summits.bed INFO @ Tue, 02 Aug 2022 09:53:32: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7723 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:53:37: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:53:37: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:53:37: #1 total tags in treatment: 15759799 INFO @ Tue, 02 Aug 2022 09:53:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:53:37: #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 09:53:37: #1 tags after filtering in treatment: 15759799 INFO @ Tue, 02 Aug 2022 09:53:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:53:37: #1 finished! INFO @ Tue, 02 Aug 2022 09:53:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:53:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:53:38: #2 number of paired peaks: 337 WARNING @ Tue, 02 Aug 2022 09:53:38: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Tue, 02 Aug 2022 09:53:38: start model_add_line... INFO @ Tue, 02 Aug 2022 09:53:38: start X-correlation... INFO @ Tue, 02 Aug 2022 09:53:38: end of X-cor INFO @ Tue, 02 Aug 2022 09:53:38: #2 finished! INFO @ Tue, 02 Aug 2022 09:53:38: #2 predicted fragment length is 107 bps INFO @ Tue, 02 Aug 2022 09:53:38: #2 alternative fragment length(s) may be 4,94,107 bps INFO @ Tue, 02 Aug 2022 09:53:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.20_model.r WARNING @ Tue, 02 Aug 2022 09:53:38: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:53:38: #2 You may need to consider one of the other alternative d(s): 4,94,107 WARNING @ Tue, 02 Aug 2022 09:53:38: #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 09:53:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:53:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:53:53: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:54:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:54:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:54:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.10_summits.bed INFO @ Tue, 02 Aug 2022 09:54:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2693 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:54:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:54:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:54:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:54:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10274854/SRX10274854.20_summits.bed INFO @ Tue, 02 Aug 2022 09:54:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (618 records, 4 fields): 21 millis CompletedMACS2peakCalling