Job ID = 16432846 SRX = SRX10274855 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18737772 spots for SRR13895161/SRR13895161.sra Written 18737772 spots for SRR13895161/SRR13895161.sra fastq に変換しました。 bowtie でマッピング中... Your job 16433882 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:55 18737772 reads; of these: 18737772 (100.00%) were unpaired; of these: 2137261 (11.41%) aligned 0 times 13626886 (72.72%) aligned exactly 1 time 2973625 (15.87%) aligned >1 times 88.59% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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] 2235676 / 16600511 = 0.1347 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 09:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.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 09:46:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:46:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:47:09: 1000000 INFO @ Tue, 02 Aug 2022 09:47:19: 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 09:47:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.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 09:47:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:47:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:47:29: 3000000 INFO @ Tue, 02 Aug 2022 09:47:39: 1000000 INFO @ Tue, 02 Aug 2022 09:47:40: 4000000 INFO @ Tue, 02 Aug 2022 09:47:51: 2000000 INFO @ Tue, 02 Aug 2022 09:47:51: 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 09:47:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.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 09:47:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:47:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:48:02: 6000000 INFO @ Tue, 02 Aug 2022 09:48:02: 3000000 INFO @ Tue, 02 Aug 2022 09:48:07: 1000000 INFO @ Tue, 02 Aug 2022 09:48:13: 7000000 INFO @ Tue, 02 Aug 2022 09:48:13: 4000000 INFO @ Tue, 02 Aug 2022 09:48:17: 2000000 INFO @ Tue, 02 Aug 2022 09:48:24: 8000000 INFO @ Tue, 02 Aug 2022 09:48:25: 5000000 INFO @ Tue, 02 Aug 2022 09:48:26: 3000000 INFO @ Tue, 02 Aug 2022 09:48:35: 9000000 INFO @ Tue, 02 Aug 2022 09:48:36: 4000000 INFO @ Tue, 02 Aug 2022 09:48:37: 6000000 INFO @ Tue, 02 Aug 2022 09:48:45: 5000000 INFO @ Tue, 02 Aug 2022 09:48:46: 10000000 INFO @ Tue, 02 Aug 2022 09:48:48: 7000000 INFO @ Tue, 02 Aug 2022 09:48:55: 6000000 INFO @ Tue, 02 Aug 2022 09:48:57: 11000000 INFO @ Tue, 02 Aug 2022 09:49:00: 8000000 INFO @ Tue, 02 Aug 2022 09:49:04: 7000000 INFO @ Tue, 02 Aug 2022 09:49:08: 12000000 INFO @ Tue, 02 Aug 2022 09:49:11: 9000000 INFO @ Tue, 02 Aug 2022 09:49:14: 8000000 INFO @ Tue, 02 Aug 2022 09:49:20: 13000000 INFO @ Tue, 02 Aug 2022 09:49:23: 10000000 INFO @ Tue, 02 Aug 2022 09:49:24: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:49:32: 14000000 INFO @ Tue, 02 Aug 2022 09:49:34: 10000000 INFO @ Tue, 02 Aug 2022 09:49:35: 11000000 INFO @ Tue, 02 Aug 2022 09:49:36: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:49:36: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:49:36: #1 total tags in treatment: 14364835 INFO @ Tue, 02 Aug 2022 09:49:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:49:36: #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 09:49:36: #1 tags after filtering in treatment: 14364835 INFO @ Tue, 02 Aug 2022 09:49:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:49:36: #1 finished! INFO @ Tue, 02 Aug 2022 09:49:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:49:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:49:37: #2 number of paired peaks: 288 WARNING @ Tue, 02 Aug 2022 09:49:37: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 02 Aug 2022 09:49:37: start model_add_line... INFO @ Tue, 02 Aug 2022 09:49:37: start X-correlation... INFO @ Tue, 02 Aug 2022 09:49:38: end of X-cor INFO @ Tue, 02 Aug 2022 09:49:38: #2 finished! INFO @ Tue, 02 Aug 2022 09:49:38: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 09:49:38: #2 alternative fragment length(s) may be 3,74 bps INFO @ Tue, 02 Aug 2022 09:49:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.05_model.r WARNING @ Tue, 02 Aug 2022 09:49:38: #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 09:49:38: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Tue, 02 Aug 2022 09:49:38: #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 09:49:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:49:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:49:43: 11000000 INFO @ Tue, 02 Aug 2022 09:49:46: 12000000 INFO @ Tue, 02 Aug 2022 09:49:52: 12000000 INFO @ Tue, 02 Aug 2022 09:49:58: 13000000 INFO @ Tue, 02 Aug 2022 09:50:01: 13000000 INFO @ Tue, 02 Aug 2022 09:50:09: 14000000 INFO @ Tue, 02 Aug 2022 09:50:11: 14000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:50:13: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:50:13: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:50:13: #1 total tags in treatment: 14364835 INFO @ Tue, 02 Aug 2022 09:50:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:50:13: #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 09:50:13: #1 tags after filtering in treatment: 14364835 INFO @ Tue, 02 Aug 2022 09:50:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:50:13: #1 finished! INFO @ Tue, 02 Aug 2022 09:50:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:50:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:50:14: #2 number of paired peaks: 288 WARNING @ Tue, 02 Aug 2022 09:50:14: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 02 Aug 2022 09:50:14: start model_add_line... INFO @ Tue, 02 Aug 2022 09:50:14: start X-correlation... INFO @ Tue, 02 Aug 2022 09:50:14: end of X-cor INFO @ Tue, 02 Aug 2022 09:50:14: #2 finished! INFO @ Tue, 02 Aug 2022 09:50:14: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 09:50:14: #2 alternative fragment length(s) may be 3,74 bps INFO @ Tue, 02 Aug 2022 09:50:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.20_model.r WARNING @ Tue, 02 Aug 2022 09:50:14: #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 09:50:14: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Tue, 02 Aug 2022 09:50:14: #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 09:50:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:50:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:50:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:50:15: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:50:15: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:50:15: #1 total tags in treatment: 14364835 INFO @ Tue, 02 Aug 2022 09:50:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:50:15: #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 09:50:15: #1 tags after filtering in treatment: 14364835 INFO @ Tue, 02 Aug 2022 09:50:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:50:15: #1 finished! INFO @ Tue, 02 Aug 2022 09:50:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:50:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:50:16: #2 number of paired peaks: 288 WARNING @ Tue, 02 Aug 2022 09:50:16: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 02 Aug 2022 09:50:16: start model_add_line... INFO @ Tue, 02 Aug 2022 09:50:17: start X-correlation... INFO @ Tue, 02 Aug 2022 09:50:17: end of X-cor INFO @ Tue, 02 Aug 2022 09:50:17: #2 finished! INFO @ Tue, 02 Aug 2022 09:50:17: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 09:50:17: #2 alternative fragment length(s) may be 3,74 bps INFO @ Tue, 02 Aug 2022 09:50:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.10_model.r WARNING @ Tue, 02 Aug 2022 09:50:17: #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 09:50:17: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Tue, 02 Aug 2022 09:50:17: #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 09:50:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:50:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.05_summits.bed INFO @ Tue, 02 Aug 2022 09:50:33: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (918 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:50:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:50:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:51:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:51:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:51:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.20_summits.bed INFO @ Tue, 02 Aug 2022 09:51:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:51:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:51:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:51:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10274855/SRX10274855.10_summits.bed INFO @ Tue, 02 Aug 2022 09:51:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (457 records, 4 fields): 9 millis CompletedMACS2peakCalling