Job ID = 14159774 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 14160305 ("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: 00:03:59 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: 00:03:59 Overall time: 00:03:59 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:36:54: # 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, 09 Dec 2021 00:36:54: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:36:54: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:37:00: 1000000 INFO @ Thu, 09 Dec 2021 00:37:06: 2000000 INFO @ Thu, 09 Dec 2021 00:37:12: 3000000 INFO @ Thu, 09 Dec 2021 00:37:17: 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 00:37:23: # 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, 09 Dec 2021 00:37:23: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:37:23: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:37:23: 5000000 INFO @ Thu, 09 Dec 2021 00:37:28: 1000000 INFO @ Thu, 09 Dec 2021 00:37:30: 6000000 INFO @ Thu, 09 Dec 2021 00:37:34: 2000000 INFO @ Thu, 09 Dec 2021 00:37:36: 7000000 INFO @ Thu, 09 Dec 2021 00:37:39: 3000000 INFO @ Thu, 09 Dec 2021 00:37:43: 8000000 INFO @ Thu, 09 Dec 2021 00:37:45: 4000000 INFO @ Thu, 09 Dec 2021 00:37:49: 9000000 INFO @ Thu, 09 Dec 2021 00:37:50: 5000000 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 00:37:53: # 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, 09 Dec 2021 00:37:53: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:37:53: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:37:55: 10000000 INFO @ Thu, 09 Dec 2021 00:37:56: 6000000 INFO @ Thu, 09 Dec 2021 00:38:00: 1000000 INFO @ Thu, 09 Dec 2021 00:38:01: 7000000 INFO @ Thu, 09 Dec 2021 00:38:02: 11000000 INFO @ Thu, 09 Dec 2021 00:38:06: 2000000 INFO @ Thu, 09 Dec 2021 00:38:07: 8000000 INFO @ Thu, 09 Dec 2021 00:38:08: 12000000 INFO @ Thu, 09 Dec 2021 00:38:12: 9000000 INFO @ Thu, 09 Dec 2021 00:38:13: 3000000 INFO @ Thu, 09 Dec 2021 00:38:15: 13000000 INFO @ Thu, 09 Dec 2021 00:38:18: 10000000 INFO @ Thu, 09 Dec 2021 00:38:19: 4000000 INFO @ Thu, 09 Dec 2021 00:38:21: 14000000 INFO @ Thu, 09 Dec 2021 00:38:23: 11000000 INFO @ Thu, 09 Dec 2021 00:38:25: 5000000 INFO @ Thu, 09 Dec 2021 00:38:27: 15000000 INFO @ Thu, 09 Dec 2021 00:38:29: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 00:38:29: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 00:38:29: #1 total tags in treatment: 15224423 INFO @ Thu, 09 Dec 2021 00:38:29: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:38:29: #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 00:38:29: 12000000 INFO @ Thu, 09 Dec 2021 00:38:29: #1 tags after filtering in treatment: 15224423 INFO @ Thu, 09 Dec 2021 00:38:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:38:29: #1 finished! INFO @ Thu, 09 Dec 2021 00:38:29: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:38:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:38:30: #2 number of paired peaks: 906 WARNING @ Thu, 09 Dec 2021 00:38:30: 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, 09 Dec 2021 00:38:30: start model_add_line... INFO @ Thu, 09 Dec 2021 00:38:30: start X-correlation... INFO @ Thu, 09 Dec 2021 00:38:30: end of X-cor INFO @ Thu, 09 Dec 2021 00:38:30: #2 finished! INFO @ Thu, 09 Dec 2021 00:38:30: #2 predicted fragment length is 177 bps INFO @ Thu, 09 Dec 2021 00:38:30: #2 alternative fragment length(s) may be 4,177 bps INFO @ Thu, 09 Dec 2021 00:38:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.05_model.r INFO @ Thu, 09 Dec 2021 00:38:30: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:38:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:38:32: 6000000 INFO @ Thu, 09 Dec 2021 00:38:34: 13000000 INFO @ Thu, 09 Dec 2021 00:38:38: 7000000 INFO @ Thu, 09 Dec 2021 00:38:40: 14000000 INFO @ Thu, 09 Dec 2021 00:38:45: 8000000 INFO @ Thu, 09 Dec 2021 00:38:45: 15000000 INFO @ Thu, 09 Dec 2021 00:38:47: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 00:38:47: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 00:38:47: #1 total tags in treatment: 15224423 INFO @ Thu, 09 Dec 2021 00:38:47: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:38:47: #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 00:38:47: #1 tags after filtering in treatment: 15224423 INFO @ Thu, 09 Dec 2021 00:38:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:38:47: #1 finished! INFO @ Thu, 09 Dec 2021 00:38:47: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:38:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:38:48: #2 number of paired peaks: 906 WARNING @ Thu, 09 Dec 2021 00:38:48: 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, 09 Dec 2021 00:38:48: start model_add_line... INFO @ Thu, 09 Dec 2021 00:38:48: start X-correlation... INFO @ Thu, 09 Dec 2021 00:38:48: end of X-cor INFO @ Thu, 09 Dec 2021 00:38:48: #2 finished! INFO @ Thu, 09 Dec 2021 00:38:48: #2 predicted fragment length is 177 bps INFO @ Thu, 09 Dec 2021 00:38:48: #2 alternative fragment length(s) may be 4,177 bps INFO @ Thu, 09 Dec 2021 00:38:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.10_model.r INFO @ Thu, 09 Dec 2021 00:38:48: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:38:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:38:51: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:38:57: 10000000 INFO @ Thu, 09 Dec 2021 00:39:02: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:39:03: 11000000 INFO @ Thu, 09 Dec 2021 00:39:09: 12000000 INFO @ Thu, 09 Dec 2021 00:39:15: 13000000 INFO @ Thu, 09 Dec 2021 00:39:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:39:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:39:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.05_summits.bed INFO @ Thu, 09 Dec 2021 00:39:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (8947 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:39:21: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:39:21: 14000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:39:27: 15000000 INFO @ Thu, 09 Dec 2021 00:39:29: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 00:39:29: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 00:39:29: #1 total tags in treatment: 15224423 INFO @ Thu, 09 Dec 2021 00:39:29: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:39:29: #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 00:39:29: #1 tags after filtering in treatment: 15224423 INFO @ Thu, 09 Dec 2021 00:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:39:29: #1 finished! INFO @ Thu, 09 Dec 2021 00:39:29: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:39:30: #2 number of paired peaks: 906 WARNING @ Thu, 09 Dec 2021 00:39:30: 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, 09 Dec 2021 00:39:30: start model_add_line... INFO @ Thu, 09 Dec 2021 00:39:30: start X-correlation... INFO @ Thu, 09 Dec 2021 00:39:30: end of X-cor INFO @ Thu, 09 Dec 2021 00:39:30: #2 finished! INFO @ Thu, 09 Dec 2021 00:39:30: #2 predicted fragment length is 177 bps INFO @ Thu, 09 Dec 2021 00:39:30: #2 alternative fragment length(s) may be 4,177 bps INFO @ Thu, 09 Dec 2021 00:39:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.20_model.r INFO @ Thu, 09 Dec 2021 00:39:30: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:39:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:39:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:39:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.10_summits.bed INFO @ Thu, 09 Dec 2021 00:39:36: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6653 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:40:02: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:40:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:40:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:40:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832066/SRX8832066.20_summits.bed INFO @ Thu, 09 Dec 2021 00:40:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3857 records, 4 fields): 5 millis CompletedMACS2peakCalling