Job ID = 14160541 SRX = SRX10399001 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13080384 spots for SRR14022426/SRR14022426.sra Written 13080384 spots for SRR14022426/SRR14022426.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160664 ("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: 00:04:29 13080384 reads; of these: 13080384 (100.00%) were unpaired; of these: 1301739 (9.95%) aligned 0 times 9820356 (75.08%) aligned exactly 1 time 1958289 (14.97%) aligned >1 times 90.05% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:29 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] 1120373 / 11778645 = 0.0951 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 03:14:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.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 03:14:42: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:14:42: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:14:49: 1000000 INFO @ Thu, 09 Dec 2021 03:14:55: 2000000 INFO @ Thu, 09 Dec 2021 03:15:01: 3000000 INFO @ Thu, 09 Dec 2021 03:15:07: 4000000 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 03:15:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.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 03:15:12: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:15:12: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:15:14: 5000000 INFO @ Thu, 09 Dec 2021 03:15:21: 1000000 INFO @ Thu, 09 Dec 2021 03:15:22: 6000000 INFO @ Thu, 09 Dec 2021 03:15:29: 2000000 INFO @ Thu, 09 Dec 2021 03:15:30: 7000000 INFO @ Thu, 09 Dec 2021 03:15:37: 8000000 INFO @ Thu, 09 Dec 2021 03:15:37: 3000000 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 03:15:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.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 03:15:42: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:15:42: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:15:45: 9000000 INFO @ Thu, 09 Dec 2021 03:15:45: 4000000 INFO @ Thu, 09 Dec 2021 03:15:50: 1000000 INFO @ Thu, 09 Dec 2021 03:15:53: 10000000 INFO @ Thu, 09 Dec 2021 03:15:54: 5000000 INFO @ Thu, 09 Dec 2021 03:15:58: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:15:58: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:15:58: #1 total tags in treatment: 10658272 INFO @ Thu, 09 Dec 2021 03:15:58: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:15:58: #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 03:15:58: #1 tags after filtering in treatment: 10658272 INFO @ Thu, 09 Dec 2021 03:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:15:58: #1 finished! INFO @ Thu, 09 Dec 2021 03:15:58: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:15:58: 2000000 INFO @ Thu, 09 Dec 2021 03:15:59: #2 number of paired peaks: 320 WARNING @ Thu, 09 Dec 2021 03:15:59: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Thu, 09 Dec 2021 03:15:59: start model_add_line... INFO @ Thu, 09 Dec 2021 03:15:59: start X-correlation... INFO @ Thu, 09 Dec 2021 03:15:59: end of X-cor INFO @ Thu, 09 Dec 2021 03:15:59: #2 finished! INFO @ Thu, 09 Dec 2021 03:15:59: #2 predicted fragment length is 73 bps INFO @ Thu, 09 Dec 2021 03:15:59: #2 alternative fragment length(s) may be 4,73 bps INFO @ Thu, 09 Dec 2021 03:15:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.05_model.r WARNING @ Thu, 09 Dec 2021 03:15:59: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:15:59: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Thu, 09 Dec 2021 03:15:59: #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 03:15:59: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:15:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:16:02: 6000000 INFO @ Thu, 09 Dec 2021 03:16:05: 3000000 INFO @ Thu, 09 Dec 2021 03:16:10: 7000000 INFO @ Thu, 09 Dec 2021 03:16:13: 4000000 INFO @ Thu, 09 Dec 2021 03:16:18: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:16:18: 8000000 INFO @ Thu, 09 Dec 2021 03:16:20: 5000000 INFO @ Thu, 09 Dec 2021 03:16:27: 9000000 INFO @ Thu, 09 Dec 2021 03:16:28: 6000000 INFO @ Thu, 09 Dec 2021 03:16:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:16:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:16:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.05_summits.bed INFO @ Thu, 09 Dec 2021 03:16:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (629 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:16:35: 10000000 INFO @ Thu, 09 Dec 2021 03:16:35: 7000000 INFO @ Thu, 09 Dec 2021 03:16:40: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:16:40: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:16:40: #1 total tags in treatment: 10658272 INFO @ Thu, 09 Dec 2021 03:16:40: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:16:40: #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 03:16:40: #1 tags after filtering in treatment: 10658272 INFO @ Thu, 09 Dec 2021 03:16:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:16:40: #1 finished! INFO @ Thu, 09 Dec 2021 03:16:40: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:16:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:16:41: #2 number of paired peaks: 320 WARNING @ Thu, 09 Dec 2021 03:16:41: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Thu, 09 Dec 2021 03:16:41: start model_add_line... INFO @ Thu, 09 Dec 2021 03:16:41: start X-correlation... INFO @ Thu, 09 Dec 2021 03:16:41: end of X-cor INFO @ Thu, 09 Dec 2021 03:16:41: #2 finished! INFO @ Thu, 09 Dec 2021 03:16:41: #2 predicted fragment length is 73 bps INFO @ Thu, 09 Dec 2021 03:16:41: #2 alternative fragment length(s) may be 4,73 bps INFO @ Thu, 09 Dec 2021 03:16:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.10_model.r WARNING @ Thu, 09 Dec 2021 03:16:41: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:16:41: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Thu, 09 Dec 2021 03:16:41: #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 03:16:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:16:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:16:43: 8000000 INFO @ Thu, 09 Dec 2021 03:16:49: 9000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:16:56: 10000000 INFO @ Thu, 09 Dec 2021 03:17:00: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:17:00: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:17:00: #1 total tags in treatment: 10658272 INFO @ Thu, 09 Dec 2021 03:17:00: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:17:00: #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 03:17:01: #1 tags after filtering in treatment: 10658272 INFO @ Thu, 09 Dec 2021 03:17:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:17:01: #1 finished! INFO @ Thu, 09 Dec 2021 03:17:01: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:17:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:17:01: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:17:01: #2 number of paired peaks: 320 WARNING @ Thu, 09 Dec 2021 03:17:01: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Thu, 09 Dec 2021 03:17:01: start model_add_line... INFO @ Thu, 09 Dec 2021 03:17:01: start X-correlation... INFO @ Thu, 09 Dec 2021 03:17:01: end of X-cor INFO @ Thu, 09 Dec 2021 03:17:01: #2 finished! INFO @ Thu, 09 Dec 2021 03:17:01: #2 predicted fragment length is 73 bps INFO @ Thu, 09 Dec 2021 03:17:01: #2 alternative fragment length(s) may be 4,73 bps INFO @ Thu, 09 Dec 2021 03:17:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.20_model.r WARNING @ Thu, 09 Dec 2021 03:17:01: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:17:01: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Thu, 09 Dec 2021 03:17:01: #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 03:17:01: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:17:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:17:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:17:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:17:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.10_summits.bed INFO @ Thu, 09 Dec 2021 03:17:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:17:22: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:17:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:17:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:17:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399001/SRX10399001.20_summits.bed INFO @ Thu, 09 Dec 2021 03:17:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (215 records, 4 fields): 1 millis CompletedMACS2peakCalling