Job ID = 14160592 SRX = SRX10399030 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19213797 spots for SRR14022418/SRR14022418.sra Written 19213797 spots for SRR14022418/SRR14022418.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160723 ("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: 00:05:49 19213797 reads; of these: 19213797 (100.00%) were unpaired; of these: 1983365 (10.32%) aligned 0 times 14209650 (73.96%) aligned exactly 1 time 3020782 (15.72%) aligned >1 times 89.68% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 2066550 / 17230432 = 0.1199 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 03:30:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.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 03:30:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:30:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:30:16: 1000000 INFO @ Thu, 09 Dec 2021 03:30:22: 2000000 INFO @ Thu, 09 Dec 2021 03:30:28: 3000000 INFO @ Thu, 09 Dec 2021 03:30:34: 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 03:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.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 03:30:39: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:30:39: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:30:40: 5000000 INFO @ Thu, 09 Dec 2021 03:30:46: 1000000 INFO @ Thu, 09 Dec 2021 03:30:46: 6000000 INFO @ Thu, 09 Dec 2021 03:30:52: 7000000 INFO @ Thu, 09 Dec 2021 03:30:52: 2000000 INFO @ Thu, 09 Dec 2021 03:30:58: 8000000 INFO @ Thu, 09 Dec 2021 03:30:58: 3000000 INFO @ Thu, 09 Dec 2021 03:31:04: 9000000 INFO @ Thu, 09 Dec 2021 03:31:04: 4000000 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 03:31:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.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 03:31:11: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:31:11: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:31:11: 10000000 INFO @ Thu, 09 Dec 2021 03:31:12: 5000000 INFO @ Thu, 09 Dec 2021 03:31:17: 1000000 INFO @ Thu, 09 Dec 2021 03:31:18: 11000000 INFO @ Thu, 09 Dec 2021 03:31:20: 6000000 INFO @ Thu, 09 Dec 2021 03:31:23: 2000000 INFO @ Thu, 09 Dec 2021 03:31:27: 12000000 INFO @ Thu, 09 Dec 2021 03:31:28: 7000000 INFO @ Thu, 09 Dec 2021 03:31:29: 3000000 INFO @ Thu, 09 Dec 2021 03:31:35: 4000000 INFO @ Thu, 09 Dec 2021 03:31:35: 13000000 INFO @ Thu, 09 Dec 2021 03:31:36: 8000000 INFO @ Thu, 09 Dec 2021 03:31:41: 5000000 INFO @ Thu, 09 Dec 2021 03:31:43: 14000000 INFO @ Thu, 09 Dec 2021 03:31:44: 9000000 INFO @ Thu, 09 Dec 2021 03:31:49: 6000000 INFO @ Thu, 09 Dec 2021 03:31:51: 10000000 INFO @ Thu, 09 Dec 2021 03:31:51: 15000000 INFO @ Thu, 09 Dec 2021 03:31:53: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:31:53: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:31:53: #1 total tags in treatment: 15163882 INFO @ Thu, 09 Dec 2021 03:31:53: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:31:53: #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 03:31:53: #1 tags after filtering in treatment: 15163882 INFO @ Thu, 09 Dec 2021 03:31:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:31:53: #1 finished! INFO @ Thu, 09 Dec 2021 03:31:53: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:31:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:31:54: #2 number of paired peaks: 266 WARNING @ Thu, 09 Dec 2021 03:31:54: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Thu, 09 Dec 2021 03:31:54: start model_add_line... INFO @ Thu, 09 Dec 2021 03:31:54: start X-correlation... INFO @ Thu, 09 Dec 2021 03:31:54: end of X-cor INFO @ Thu, 09 Dec 2021 03:31:54: #2 finished! INFO @ Thu, 09 Dec 2021 03:31:54: #2 predicted fragment length is 73 bps INFO @ Thu, 09 Dec 2021 03:31:54: #2 alternative fragment length(s) may be 3,73 bps INFO @ Thu, 09 Dec 2021 03:31:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.05_model.r WARNING @ Thu, 09 Dec 2021 03:31:54: #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 03:31:54: #2 You may need to consider one of the other alternative d(s): 3,73 WARNING @ Thu, 09 Dec 2021 03:31:54: #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 03:31:54: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:31:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:31:56: 7000000 INFO @ Thu, 09 Dec 2021 03:31:57: 11000000 INFO @ Thu, 09 Dec 2021 03:32:02: 8000000 INFO @ Thu, 09 Dec 2021 03:32:05: 12000000 INFO @ Thu, 09 Dec 2021 03:32:10: 9000000 INFO @ Thu, 09 Dec 2021 03:32:12: 13000000 INFO @ Thu, 09 Dec 2021 03:32:18: 10000000 INFO @ Thu, 09 Dec 2021 03:32:20: 14000000 INFO @ Thu, 09 Dec 2021 03:32:27: 11000000 INFO @ Thu, 09 Dec 2021 03:32:28: 15000000 INFO @ Thu, 09 Dec 2021 03:32:29: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:32:29: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:32:29: #1 total tags in treatment: 15163882 INFO @ Thu, 09 Dec 2021 03:32:29: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:32:29: #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 03:32:29: #1 tags after filtering in treatment: 15163882 INFO @ Thu, 09 Dec 2021 03:32:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:32:29: #1 finished! INFO @ Thu, 09 Dec 2021 03:32:29: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:32:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:32:30: #2 number of paired peaks: 266 WARNING @ Thu, 09 Dec 2021 03:32:30: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Thu, 09 Dec 2021 03:32:30: start model_add_line... INFO @ Thu, 09 Dec 2021 03:32:30: start X-correlation... INFO @ Thu, 09 Dec 2021 03:32:30: end of X-cor INFO @ Thu, 09 Dec 2021 03:32:30: #2 finished! INFO @ Thu, 09 Dec 2021 03:32:30: #2 predicted fragment length is 73 bps INFO @ Thu, 09 Dec 2021 03:32:30: #2 alternative fragment length(s) may be 3,73 bps INFO @ Thu, 09 Dec 2021 03:32:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.10_model.r WARNING @ Thu, 09 Dec 2021 03:32:30: #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 03:32:30: #2 You may need to consider one of the other alternative d(s): 3,73 WARNING @ Thu, 09 Dec 2021 03:32:30: #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 03:32:30: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:32:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:32:31: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:32:36: 12000000 INFO @ Thu, 09 Dec 2021 03:32:43: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:32:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:32:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:32:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.05_summits.bed INFO @ Thu, 09 Dec 2021 03:32:48: Done! pass1 - making usageList (7 chroms): 18 millis pass2 - checking and writing primary data (1078 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:32:50: 14000000 INFO @ Thu, 09 Dec 2021 03:32:56: 15000000 INFO @ Thu, 09 Dec 2021 03:32:57: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:32:57: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:32:57: #1 total tags in treatment: 15163882 INFO @ Thu, 09 Dec 2021 03:32:57: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:32:57: #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 03:32:57: #1 tags after filtering in treatment: 15163882 INFO @ Thu, 09 Dec 2021 03:32:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:32:57: #1 finished! INFO @ Thu, 09 Dec 2021 03:32:57: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:32:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:32:58: #2 number of paired peaks: 266 WARNING @ Thu, 09 Dec 2021 03:32:58: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Thu, 09 Dec 2021 03:32:58: start model_add_line... INFO @ Thu, 09 Dec 2021 03:32:58: start X-correlation... INFO @ Thu, 09 Dec 2021 03:32:58: end of X-cor INFO @ Thu, 09 Dec 2021 03:32:58: #2 finished! INFO @ Thu, 09 Dec 2021 03:32:58: #2 predicted fragment length is 73 bps INFO @ Thu, 09 Dec 2021 03:32:58: #2 alternative fragment length(s) may be 3,73 bps INFO @ Thu, 09 Dec 2021 03:32:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.20_model.r WARNING @ Thu, 09 Dec 2021 03:32:58: #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 03:32:58: #2 You may need to consider one of the other alternative d(s): 3,73 WARNING @ Thu, 09 Dec 2021 03:32:58: #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 03:32:58: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:32:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:33:02: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:33:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:33:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:33:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.10_summits.bed INFO @ Thu, 09 Dec 2021 03:33:17: Done! pass1 - making usageList (7 chroms): 35 millis pass2 - checking and writing primary data (511 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:33:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:33:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:33:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:33:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399030/SRX10399030.20_summits.bed INFO @ Thu, 09 Dec 2021 03:33:51: Done! pass1 - making usageList (6 chroms): 21 millis pass2 - checking and writing primary data (246 records, 4 fields): 28 millis CompletedMACS2peakCalling