Job ID = 16434863 SRX = SRX10435525 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21755740 spots for SRR14060925/SRR14060925.sra Written 21755740 spots for SRR14060925/SRR14060925.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434919 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:27 21755740 reads; of these: 21755740 (100.00%) were unpaired; of these: 5756396 (26.46%) aligned 0 times 13664920 (62.81%) aligned exactly 1 time 2334424 (10.73%) aligned >1 times 73.54% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 2049306 / 15999344 = 0.1281 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 10:15:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.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 10:15:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:15:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:15:18: 1000000 INFO @ Tue, 02 Aug 2022 10:15:24: 2000000 INFO @ Tue, 02 Aug 2022 10:15:31: 3000000 INFO @ Tue, 02 Aug 2022 10:15:36: 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 10:15:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.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 10:15:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:15:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:15:43: 5000000 INFO @ Tue, 02 Aug 2022 10:15:49: 1000000 INFO @ Tue, 02 Aug 2022 10:15:49: 6000000 INFO @ Tue, 02 Aug 2022 10:15:56: 2000000 INFO @ Tue, 02 Aug 2022 10:15:56: 7000000 INFO @ Tue, 02 Aug 2022 10:16:02: 8000000 INFO @ Tue, 02 Aug 2022 10:16:02: 3000000 INFO @ Tue, 02 Aug 2022 10:16:08: 9000000 INFO @ Tue, 02 Aug 2022 10:16:09: 4000000 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 10:16:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.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 10:16:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:16:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:16:15: 10000000 INFO @ Tue, 02 Aug 2022 10:16:17: 5000000 INFO @ Tue, 02 Aug 2022 10:16:19: 1000000 INFO @ Tue, 02 Aug 2022 10:16:21: 11000000 INFO @ Tue, 02 Aug 2022 10:16:24: 6000000 INFO @ Tue, 02 Aug 2022 10:16:25: 2000000 INFO @ Tue, 02 Aug 2022 10:16:28: 12000000 INFO @ Tue, 02 Aug 2022 10:16:31: 7000000 INFO @ Tue, 02 Aug 2022 10:16:32: 3000000 INFO @ Tue, 02 Aug 2022 10:16:34: 13000000 INFO @ Tue, 02 Aug 2022 10:16:38: 8000000 INFO @ Tue, 02 Aug 2022 10:16:39: 4000000 INFO @ Tue, 02 Aug 2022 10:16:40: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:16:40: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:16:40: #1 total tags in treatment: 13950038 INFO @ Tue, 02 Aug 2022 10:16:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:16:40: #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 10:16:41: #1 tags after filtering in treatment: 13950038 INFO @ Tue, 02 Aug 2022 10:16:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:16:41: #1 finished! INFO @ Tue, 02 Aug 2022 10:16:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:16:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:16:41: #2 number of paired peaks: 439 WARNING @ Tue, 02 Aug 2022 10:16:41: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Tue, 02 Aug 2022 10:16:41: start model_add_line... INFO @ Tue, 02 Aug 2022 10:16:42: start X-correlation... INFO @ Tue, 02 Aug 2022 10:16:42: end of X-cor INFO @ Tue, 02 Aug 2022 10:16:42: #2 finished! INFO @ Tue, 02 Aug 2022 10:16:42: #2 predicted fragment length is 129 bps INFO @ Tue, 02 Aug 2022 10:16:42: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 02 Aug 2022 10:16:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.05_model.r WARNING @ Tue, 02 Aug 2022 10:16:42: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:16:42: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Tue, 02 Aug 2022 10:16:42: #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 10:16:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:16:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:16:45: 9000000 INFO @ Tue, 02 Aug 2022 10:16:46: 5000000 INFO @ Tue, 02 Aug 2022 10:16:52: 10000000 INFO @ Tue, 02 Aug 2022 10:16:53: 6000000 INFO @ Tue, 02 Aug 2022 10:16:59: 11000000 INFO @ Tue, 02 Aug 2022 10:17:00: 7000000 INFO @ Tue, 02 Aug 2022 10:17:06: 12000000 INFO @ Tue, 02 Aug 2022 10:17:07: 8000000 INFO @ Tue, 02 Aug 2022 10:17:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:17:13: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:17:14: 9000000 INFO @ Tue, 02 Aug 2022 10:17:20: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:17:20: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:17:20: #1 total tags in treatment: 13950038 INFO @ Tue, 02 Aug 2022 10:17:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:17:20: #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 10:17:20: #1 tags after filtering in treatment: 13950038 INFO @ Tue, 02 Aug 2022 10:17:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:17:20: #1 finished! INFO @ Tue, 02 Aug 2022 10:17:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:17:21: #2 number of paired peaks: 439 WARNING @ Tue, 02 Aug 2022 10:17:21: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Tue, 02 Aug 2022 10:17:21: start model_add_line... INFO @ Tue, 02 Aug 2022 10:17:21: 10000000 INFO @ Tue, 02 Aug 2022 10:17:21: start X-correlation... INFO @ Tue, 02 Aug 2022 10:17:21: end of X-cor INFO @ Tue, 02 Aug 2022 10:17:21: #2 finished! INFO @ Tue, 02 Aug 2022 10:17:21: #2 predicted fragment length is 129 bps INFO @ Tue, 02 Aug 2022 10:17:21: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 02 Aug 2022 10:17:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.10_model.r WARNING @ Tue, 02 Aug 2022 10:17:21: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:17:21: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Tue, 02 Aug 2022 10:17:21: #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 10:17:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:17:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:17:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.05_summits.bed INFO @ Tue, 02 Aug 2022 10:17:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2389 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:17:28: 11000000 INFO @ Tue, 02 Aug 2022 10:17:34: 12000000 INFO @ Tue, 02 Aug 2022 10:17:40: 13000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:17:46: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:17:46: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:17:46: #1 total tags in treatment: 13950038 INFO @ Tue, 02 Aug 2022 10:17:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:17:46: #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 10:17:47: #1 tags after filtering in treatment: 13950038 INFO @ Tue, 02 Aug 2022 10:17:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:17:47: #1 finished! INFO @ Tue, 02 Aug 2022 10:17:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:17:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:17:48: #2 number of paired peaks: 439 WARNING @ Tue, 02 Aug 2022 10:17:48: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Tue, 02 Aug 2022 10:17:48: start model_add_line... INFO @ Tue, 02 Aug 2022 10:17:48: start X-correlation... INFO @ Tue, 02 Aug 2022 10:17:48: end of X-cor INFO @ Tue, 02 Aug 2022 10:17:48: #2 finished! INFO @ Tue, 02 Aug 2022 10:17:48: #2 predicted fragment length is 129 bps INFO @ Tue, 02 Aug 2022 10:17:48: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 02 Aug 2022 10:17:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.20_model.r WARNING @ Tue, 02 Aug 2022 10:17:48: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:17:48: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Tue, 02 Aug 2022 10:17:48: #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 10:17:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:17:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:17:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:18:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:18:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:18:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.10_summits.bed INFO @ Tue, 02 Aug 2022 10:18:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1493 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:18:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:18:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:18:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:18:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435525/SRX10435525.20_summits.bed INFO @ Tue, 02 Aug 2022 10:18:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (839 records, 4 fields): 22 millis CompletedMACS2peakCalling