Job ID = 10165695 SRX = SRX8832066 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20583358 spots for SRR12332008/SRR12332008.sra Written 20583358 spots for SRR12332008/SRR12332008.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165882 ("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: 00:04:22 20583358 reads; of these: 20583358 (100.00%) were unpaired; of these: 932921 (4.53%) aligned 0 times 16902099 (82.12%) aligned exactly 1 time 2748338 (13.35%) aligned >1 times 95.47% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 4426014 / 19650437 = 0.2252 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:45:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.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, 08 Oct 2020 19:45:52: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:45:52: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:45:57: 1000000 INFO @ Thu, 08 Oct 2020 19:46:02: 2000000 INFO @ Thu, 08 Oct 2020 19:46:07: 3000000 INFO @ Thu, 08 Oct 2020 19:46:13: 4000000 INFO @ Thu, 08 Oct 2020 19:46:18: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:46:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.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, 08 Oct 2020 19:46:21: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:46:21: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:46:23: 6000000 INFO @ Thu, 08 Oct 2020 19:46:28: 1000000 INFO @ Thu, 08 Oct 2020 19:46:30: 7000000 INFO @ Thu, 08 Oct 2020 19:46:34: 2000000 INFO @ Thu, 08 Oct 2020 19:46:36: 8000000 INFO @ Thu, 08 Oct 2020 19:46:41: 3000000 INFO @ Thu, 08 Oct 2020 19:46:42: 9000000 INFO @ Thu, 08 Oct 2020 19:46:47: 4000000 INFO @ Thu, 08 Oct 2020 19:46:48: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:46:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.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, 08 Oct 2020 19:46:51: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:46:51: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:46:53: 5000000 INFO @ Thu, 08 Oct 2020 19:46:55: 11000000 INFO @ Thu, 08 Oct 2020 19:46:59: 1000000 INFO @ Thu, 08 Oct 2020 19:47:00: 6000000 INFO @ Thu, 08 Oct 2020 19:47:02: 12000000 INFO @ Thu, 08 Oct 2020 19:47:06: 2000000 INFO @ Thu, 08 Oct 2020 19:47:07: 7000000 INFO @ Thu, 08 Oct 2020 19:47:09: 13000000 INFO @ Thu, 08 Oct 2020 19:47:12: 3000000 INFO @ Thu, 08 Oct 2020 19:47:13: 8000000 INFO @ Thu, 08 Oct 2020 19:47:16: 14000000 INFO @ Thu, 08 Oct 2020 19:47:19: 4000000 INFO @ Thu, 08 Oct 2020 19:47:20: 9000000 INFO @ Thu, 08 Oct 2020 19:47:22: 15000000 INFO @ Thu, 08 Oct 2020 19:47:24: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:47:24: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:47:24: #1 total tags in treatment: 15224423 INFO @ Thu, 08 Oct 2020 19:47:24: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:47:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:47:24: #1 tags after filtering in treatment: 15224423 INFO @ Thu, 08 Oct 2020 19:47:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:47:24: #1 finished! INFO @ Thu, 08 Oct 2020 19:47:24: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:47:25: #2 number of paired peaks: 906 WARNING @ Thu, 08 Oct 2020 19:47:25: Fewer paired peaks (906) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 906 pairs to build model! INFO @ Thu, 08 Oct 2020 19:47:25: start model_add_line... INFO @ Thu, 08 Oct 2020 19:47:26: start X-correlation... INFO @ Thu, 08 Oct 2020 19:47:26: end of X-cor INFO @ Thu, 08 Oct 2020 19:47:26: #2 finished! INFO @ Thu, 08 Oct 2020 19:47:26: #2 predicted fragment length is 177 bps INFO @ Thu, 08 Oct 2020 19:47:26: #2 alternative fragment length(s) may be 4,177 bps INFO @ Thu, 08 Oct 2020 19:47:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.05_model.r INFO @ Thu, 08 Oct 2020 19:47:26: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:47:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:47:26: 5000000 INFO @ Thu, 08 Oct 2020 19:47:27: 10000000 INFO @ Thu, 08 Oct 2020 19:47:33: 6000000 INFO @ Thu, 08 Oct 2020 19:47:34: 11000000 INFO @ Thu, 08 Oct 2020 19:47:40: 7000000 INFO @ Thu, 08 Oct 2020 19:47:41: 12000000 INFO @ Thu, 08 Oct 2020 19:47:46: 8000000 INFO @ Thu, 08 Oct 2020 19:47:48: 13000000 INFO @ Thu, 08 Oct 2020 19:47:53: 9000000 INFO @ Thu, 08 Oct 2020 19:47:55: 14000000 INFO @ Thu, 08 Oct 2020 19:48:00: 10000000 INFO @ Thu, 08 Oct 2020 19:48:01: 15000000 INFO @ Thu, 08 Oct 2020 19:48:02: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:48:03: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:48:03: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:48:03: #1 total tags in treatment: 15224423 INFO @ Thu, 08 Oct 2020 19:48:03: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:48:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:48:03: #1 tags after filtering in treatment: 15224423 INFO @ Thu, 08 Oct 2020 19:48:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:48:03: #1 finished! INFO @ Thu, 08 Oct 2020 19:48:03: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:48:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:48:04: #2 number of paired peaks: 906 WARNING @ Thu, 08 Oct 2020 19:48:04: Fewer paired peaks (906) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 906 pairs to build model! INFO @ Thu, 08 Oct 2020 19:48:04: start model_add_line... INFO @ Thu, 08 Oct 2020 19:48:05: start X-correlation... INFO @ Thu, 08 Oct 2020 19:48:05: end of X-cor INFO @ Thu, 08 Oct 2020 19:48:05: #2 finished! INFO @ Thu, 08 Oct 2020 19:48:05: #2 predicted fragment length is 177 bps INFO @ Thu, 08 Oct 2020 19:48:05: #2 alternative fragment length(s) may be 4,177 bps INFO @ Thu, 08 Oct 2020 19:48:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.10_model.r INFO @ Thu, 08 Oct 2020 19:48:05: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:48:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:48:07: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:48:14: 12000000 INFO @ Thu, 08 Oct 2020 19:48:21: 13000000 INFO @ Thu, 08 Oct 2020 19:48:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:48:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:48:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.05_summits.bed INFO @ Thu, 08 Oct 2020 19:48:21: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8947 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:48:28: 14000000 INFO @ Thu, 08 Oct 2020 19:48:34: 15000000 INFO @ Thu, 08 Oct 2020 19:48:36: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:48:36: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:48:36: #1 total tags in treatment: 15224423 INFO @ Thu, 08 Oct 2020 19:48:36: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:48:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:48:36: #1 tags after filtering in treatment: 15224423 INFO @ Thu, 08 Oct 2020 19:48:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:48:36: #1 finished! INFO @ Thu, 08 Oct 2020 19:48:36: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:48:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:48:37: #2 number of paired peaks: 906 WARNING @ Thu, 08 Oct 2020 19:48:37: Fewer paired peaks (906) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 906 pairs to build model! INFO @ Thu, 08 Oct 2020 19:48:37: start model_add_line... INFO @ Thu, 08 Oct 2020 19:48:37: start X-correlation... INFO @ Thu, 08 Oct 2020 19:48:37: end of X-cor INFO @ Thu, 08 Oct 2020 19:48:37: #2 finished! INFO @ Thu, 08 Oct 2020 19:48:37: #2 predicted fragment length is 177 bps INFO @ Thu, 08 Oct 2020 19:48:37: #2 alternative fragment length(s) may be 4,177 bps INFO @ Thu, 08 Oct 2020 19:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.20_model.r INFO @ Thu, 08 Oct 2020 19:48:37: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:48:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:48:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:48:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:48:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.10_summits.bed INFO @ Thu, 08 Oct 2020 19:48:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6653 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:49:13: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:49:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:49:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:49:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.20_summits.bed INFO @ Thu, 08 Oct 2020 19:49:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3857 records, 4 fields): 7 millis CompletedMACS2peakCalling