Job ID = 14160333 SRX = SRX9555456 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8289457 spots for SRR13111107/SRR13111107.sra Written 8289457 spots for SRR13111107/SRR13111107.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160455 ("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: 00:08:55 8289457 reads; of these: 8289457 (100.00%) were paired; of these: 742820 (8.96%) aligned concordantly 0 times 6538991 (78.88%) aligned concordantly exactly 1 time 1007646 (12.16%) aligned concordantly >1 times ---- 742820 pairs aligned concordantly 0 times; of these: 322170 (43.37%) aligned discordantly 1 time ---- 420650 pairs aligned 0 times concordantly or discordantly; of these: 841300 mates make up the pairs; of these: 539952 (64.18%) aligned 0 times 201960 (24.01%) aligned exactly 1 time 99388 (11.81%) aligned >1 times 96.74% overall alignment rate Time searching: 00:08:55 Overall time: 00:08:55 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 485893 / 7861503 = 0.0618 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 01:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.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 01:44:03: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:44:03: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:44:10: 1000000 INFO @ Thu, 09 Dec 2021 01:44:18: 2000000 INFO @ Thu, 09 Dec 2021 01:44:25: 3000000 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 01:44:32: 4000000 INFO @ Thu, 09 Dec 2021 01:44:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.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 01:44:33: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:44:33: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:44:39: 5000000 INFO @ Thu, 09 Dec 2021 01:44:42: 1000000 INFO @ Thu, 09 Dec 2021 01:44:47: 6000000 INFO @ Thu, 09 Dec 2021 01:44:51: 2000000 INFO @ Thu, 09 Dec 2021 01:44:54: 7000000 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 01:45:00: 3000000 INFO @ Thu, 09 Dec 2021 01:45:01: 8000000 INFO @ Thu, 09 Dec 2021 01:45:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.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 01:45:03: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:45:03: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:45:08: 9000000 INFO @ Thu, 09 Dec 2021 01:45:10: 4000000 INFO @ Thu, 09 Dec 2021 01:45:11: 1000000 INFO @ Thu, 09 Dec 2021 01:45:15: 10000000 INFO @ Thu, 09 Dec 2021 01:45:19: 5000000 INFO @ Thu, 09 Dec 2021 01:45:19: 2000000 INFO @ Thu, 09 Dec 2021 01:45:23: 11000000 INFO @ Thu, 09 Dec 2021 01:45:28: 6000000 INFO @ Thu, 09 Dec 2021 01:45:28: 3000000 INFO @ Thu, 09 Dec 2021 01:45:30: 12000000 INFO @ Thu, 09 Dec 2021 01:45:36: 4000000 INFO @ Thu, 09 Dec 2021 01:45:37: 7000000 INFO @ Thu, 09 Dec 2021 01:45:38: 13000000 INFO @ Thu, 09 Dec 2021 01:45:45: 5000000 INFO @ Thu, 09 Dec 2021 01:45:45: 14000000 INFO @ Thu, 09 Dec 2021 01:45:46: 8000000 INFO @ Thu, 09 Dec 2021 01:45:54: 15000000 INFO @ Thu, 09 Dec 2021 01:45:54: 6000000 INFO @ Thu, 09 Dec 2021 01:45:54: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:45:54: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:45:54: #1 total tags in treatment: 7072193 INFO @ Thu, 09 Dec 2021 01:45:54: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:45:54: #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 01:45:54: #1 tags after filtering in treatment: 6684658 INFO @ Thu, 09 Dec 2021 01:45:54: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 01:45:54: #1 finished! INFO @ Thu, 09 Dec 2021 01:45:54: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:45:55: #2 number of paired peaks: 430 WARNING @ Thu, 09 Dec 2021 01:45:55: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Thu, 09 Dec 2021 01:45:55: start model_add_line... INFO @ Thu, 09 Dec 2021 01:45:55: start X-correlation... INFO @ Thu, 09 Dec 2021 01:45:55: end of X-cor INFO @ Thu, 09 Dec 2021 01:45:55: #2 finished! INFO @ Thu, 09 Dec 2021 01:45:55: #2 predicted fragment length is 157 bps INFO @ Thu, 09 Dec 2021 01:45:55: #2 alternative fragment length(s) may be 4,157 bps INFO @ Thu, 09 Dec 2021 01:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.05_model.r INFO @ Thu, 09 Dec 2021 01:45:55: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:45:55: 9000000 INFO @ Thu, 09 Dec 2021 01:46:02: 7000000 INFO @ Thu, 09 Dec 2021 01:46:05: 10000000 INFO @ Thu, 09 Dec 2021 01:46:11: 8000000 INFO @ Thu, 09 Dec 2021 01:46:14: 11000000 INFO @ Thu, 09 Dec 2021 01:46:15: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:46:19: 9000000 INFO @ Thu, 09 Dec 2021 01:46:23: 12000000 INFO @ Thu, 09 Dec 2021 01:46:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:46:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:46:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.05_summits.bed INFO @ Thu, 09 Dec 2021 01:46:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:46:27: 10000000 INFO @ Thu, 09 Dec 2021 01:46:32: 13000000 INFO @ Thu, 09 Dec 2021 01:46:34: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:46:41: 14000000 INFO @ Thu, 09 Dec 2021 01:46:42: 12000000 INFO @ Thu, 09 Dec 2021 01:46:50: 13000000 INFO @ Thu, 09 Dec 2021 01:46:51: 15000000 INFO @ Thu, 09 Dec 2021 01:46:51: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:46:51: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:46:51: #1 total tags in treatment: 7072193 INFO @ Thu, 09 Dec 2021 01:46:51: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:46:51: #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 01:46:51: #1 tags after filtering in treatment: 6684658 INFO @ Thu, 09 Dec 2021 01:46:51: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 01:46:51: #1 finished! INFO @ Thu, 09 Dec 2021 01:46:51: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:46:52: #2 number of paired peaks: 430 WARNING @ Thu, 09 Dec 2021 01:46:52: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Thu, 09 Dec 2021 01:46:52: start model_add_line... INFO @ Thu, 09 Dec 2021 01:46:52: start X-correlation... INFO @ Thu, 09 Dec 2021 01:46:52: end of X-cor INFO @ Thu, 09 Dec 2021 01:46:52: #2 finished! INFO @ Thu, 09 Dec 2021 01:46:52: #2 predicted fragment length is 157 bps INFO @ Thu, 09 Dec 2021 01:46:52: #2 alternative fragment length(s) may be 4,157 bps INFO @ Thu, 09 Dec 2021 01:46:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.10_model.r INFO @ Thu, 09 Dec 2021 01:46:52: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:46:58: 14000000 INFO @ Thu, 09 Dec 2021 01:47:06: 15000000 INFO @ Thu, 09 Dec 2021 01:47:06: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:47:06: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:47:06: #1 total tags in treatment: 7072193 INFO @ Thu, 09 Dec 2021 01:47:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:47:06: #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 01:47:06: #1 tags after filtering in treatment: 6684658 INFO @ Thu, 09 Dec 2021 01:47:06: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 01:47:06: #1 finished! INFO @ Thu, 09 Dec 2021 01:47:06: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:47:07: #2 number of paired peaks: 430 WARNING @ Thu, 09 Dec 2021 01:47:07: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Thu, 09 Dec 2021 01:47:07: start model_add_line... INFO @ Thu, 09 Dec 2021 01:47:07: start X-correlation... INFO @ Thu, 09 Dec 2021 01:47:07: end of X-cor INFO @ Thu, 09 Dec 2021 01:47:07: #2 finished! INFO @ Thu, 09 Dec 2021 01:47:07: #2 predicted fragment length is 157 bps INFO @ Thu, 09 Dec 2021 01:47:07: #2 alternative fragment length(s) may be 4,157 bps INFO @ Thu, 09 Dec 2021 01:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.20_model.r INFO @ Thu, 09 Dec 2021 01:47:07: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:47:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:47:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:47:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:47:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.10_summits.bed INFO @ Thu, 09 Dec 2021 01:47:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:47:27: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:47:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:47:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:47:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555456/SRX9555456.20_summits.bed INFO @ Thu, 09 Dec 2021 01:47:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 3 millis CompletedMACS2peakCalling