Job ID = 14160573 SRX = SRX10399015 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19274405 spots for SRR14022403/SRR14022403.sra Written 19274405 spots for SRR14022403/SRR14022403.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160702 ("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: 00:06:07 19274405 reads; of these: 19274405 (100.00%) were unpaired; of these: 5875349 (30.48%) aligned 0 times 11281856 (58.53%) aligned exactly 1 time 2117200 (10.98%) aligned >1 times 69.52% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 2818969 / 13399056 = 0.2104 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 03:26:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.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 03:26:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:26:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:26:20: 1000000 INFO @ Thu, 09 Dec 2021 03:26:30: 2000000 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 03:26:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.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 03:26:39: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:26:39: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:26:40: 3000000 INFO @ Thu, 09 Dec 2021 03:26:50: 1000000 INFO @ Thu, 09 Dec 2021 03:26:50: 4000000 INFO @ Thu, 09 Dec 2021 03:27:00: 5000000 INFO @ Thu, 09 Dec 2021 03:27:00: 2000000 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 03:27:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.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 03:27:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:27:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:27:10: 6000000 INFO @ Thu, 09 Dec 2021 03:27:10: 3000000 INFO @ Thu, 09 Dec 2021 03:27:21: 7000000 INFO @ Thu, 09 Dec 2021 03:27:21: 4000000 INFO @ Thu, 09 Dec 2021 03:27:22: 1000000 INFO @ Thu, 09 Dec 2021 03:27:32: 5000000 INFO @ Thu, 09 Dec 2021 03:27:32: 8000000 INFO @ Thu, 09 Dec 2021 03:27:33: 2000000 INFO @ Thu, 09 Dec 2021 03:27:42: 6000000 INFO @ Thu, 09 Dec 2021 03:27:42: 9000000 INFO @ Thu, 09 Dec 2021 03:27:46: 3000000 INFO @ Thu, 09 Dec 2021 03:27:53: 7000000 INFO @ Thu, 09 Dec 2021 03:27:53: 10000000 INFO @ Thu, 09 Dec 2021 03:27:57: 4000000 INFO @ Thu, 09 Dec 2021 03:27:58: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:27:58: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:27:58: #1 total tags in treatment: 10580087 INFO @ Thu, 09 Dec 2021 03:27:58: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:27:58: #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 03:27:59: #1 tags after filtering in treatment: 10580087 INFO @ Thu, 09 Dec 2021 03:27:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:27:59: #1 finished! INFO @ Thu, 09 Dec 2021 03:27:59: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:27:59: #2 number of paired peaks: 536 WARNING @ Thu, 09 Dec 2021 03:27:59: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Thu, 09 Dec 2021 03:27:59: start model_add_line... INFO @ Thu, 09 Dec 2021 03:27:59: start X-correlation... INFO @ Thu, 09 Dec 2021 03:27:59: end of X-cor INFO @ Thu, 09 Dec 2021 03:27:59: #2 finished! INFO @ Thu, 09 Dec 2021 03:27:59: #2 predicted fragment length is 128 bps INFO @ Thu, 09 Dec 2021 03:27:59: #2 alternative fragment length(s) may be 128 bps INFO @ Thu, 09 Dec 2021 03:27:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.05_model.r WARNING @ Thu, 09 Dec 2021 03:28:00: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:28:00: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Thu, 09 Dec 2021 03:28:00: #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 03:28:00: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:28:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:28:03: 8000000 INFO @ Thu, 09 Dec 2021 03:28:09: 5000000 INFO @ Thu, 09 Dec 2021 03:28:13: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:28:20: 6000000 INFO @ Thu, 09 Dec 2021 03:28:23: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:28:24: 10000000 INFO @ Thu, 09 Dec 2021 03:28:30: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:28:30: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:28:30: #1 total tags in treatment: 10580087 INFO @ Thu, 09 Dec 2021 03:28:30: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:28:30: #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 03:28:30: #1 tags after filtering in treatment: 10580087 INFO @ Thu, 09 Dec 2021 03:28:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:28:30: #1 finished! INFO @ Thu, 09 Dec 2021 03:28:30: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:28:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:28:31: #2 number of paired peaks: 536 WARNING @ Thu, 09 Dec 2021 03:28:31: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Thu, 09 Dec 2021 03:28:31: start model_add_line... INFO @ Thu, 09 Dec 2021 03:28:31: start X-correlation... INFO @ Thu, 09 Dec 2021 03:28:31: end of X-cor INFO @ Thu, 09 Dec 2021 03:28:31: #2 finished! INFO @ Thu, 09 Dec 2021 03:28:31: #2 predicted fragment length is 128 bps INFO @ Thu, 09 Dec 2021 03:28:31: #2 alternative fragment length(s) may be 128 bps INFO @ Thu, 09 Dec 2021 03:28:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.10_model.r WARNING @ Thu, 09 Dec 2021 03:28:31: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:28:31: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Thu, 09 Dec 2021 03:28:31: #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 03:28:31: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:28:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:28:31: 7000000 INFO @ Thu, 09 Dec 2021 03:28:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:28:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:28:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.05_summits.bed INFO @ Thu, 09 Dec 2021 03:28:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1763 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:28:42: 8000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:28:54: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:28:54: 9000000 INFO @ Thu, 09 Dec 2021 03:29:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:29:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:29:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.10_summits.bed INFO @ Thu, 09 Dec 2021 03:29:06: Done! INFO @ Thu, 09 Dec 2021 03:29:06: 10000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1153 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:29:12: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:29:12: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:29:12: #1 total tags in treatment: 10580087 INFO @ Thu, 09 Dec 2021 03:29:12: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:29:12: #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 03:29:13: #1 tags after filtering in treatment: 10580087 INFO @ Thu, 09 Dec 2021 03:29:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:29:13: #1 finished! INFO @ Thu, 09 Dec 2021 03:29:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:29:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:29:13: #2 number of paired peaks: 536 WARNING @ Thu, 09 Dec 2021 03:29:13: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Thu, 09 Dec 2021 03:29:13: start model_add_line... INFO @ Thu, 09 Dec 2021 03:29:14: start X-correlation... INFO @ Thu, 09 Dec 2021 03:29:14: end of X-cor INFO @ Thu, 09 Dec 2021 03:29:14: #2 finished! INFO @ Thu, 09 Dec 2021 03:29:14: #2 predicted fragment length is 128 bps INFO @ Thu, 09 Dec 2021 03:29:14: #2 alternative fragment length(s) may be 128 bps INFO @ Thu, 09 Dec 2021 03:29:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.20_model.r WARNING @ Thu, 09 Dec 2021 03:29:14: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:29:14: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Thu, 09 Dec 2021 03:29:14: #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 03:29:14: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:29:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:29:37: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:29:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:29:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:29:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399015/SRX10399015.20_summits.bed INFO @ Thu, 09 Dec 2021 03:29:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (710 records, 4 fields): 3 millis CompletedMACS2peakCalling