Job ID = 14160341 SRX = SRX9555460 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26818496 spots for SRR13111111/SRR13111111.sra Written 26818496 spots for SRR13111111/SRR13111111.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160507 ("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: 00:29:16 26818496 reads; of these: 26818496 (100.00%) were paired; of these: 1559625 (5.82%) aligned concordantly 0 times 21764492 (81.15%) aligned concordantly exactly 1 time 3494379 (13.03%) aligned concordantly >1 times ---- 1559625 pairs aligned concordantly 0 times; of these: 72058 (4.62%) aligned discordantly 1 time ---- 1487567 pairs aligned 0 times concordantly or discordantly; of these: 2975134 mates make up the pairs; of these: 2739760 (92.09%) aligned 0 times 178958 (6.02%) aligned exactly 1 time 56416 (1.90%) aligned >1 times 94.89% overall alignment rate Time searching: 00:29:16 Overall time: 00:29:16 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 24 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] 7575956 / 25319708 = 0.2992 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 02:15:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.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 02:15:32: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:15:32: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:15:39: 1000000 INFO @ Thu, 09 Dec 2021 02:15:45: 2000000 INFO @ Thu, 09 Dec 2021 02:15:53: 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 02:16:00: 4000000 INFO @ Thu, 09 Dec 2021 02:16:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.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 02:16:01: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:16:01: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:16:07: 5000000 INFO @ Thu, 09 Dec 2021 02:16:08: 1000000 INFO @ Thu, 09 Dec 2021 02:16:14: 2000000 INFO @ Thu, 09 Dec 2021 02:16:15: 6000000 INFO @ Thu, 09 Dec 2021 02:16:21: 3000000 INFO @ Thu, 09 Dec 2021 02:16:22: 7000000 INFO @ Thu, 09 Dec 2021 02:16:27: 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 02:16:29: 8000000 INFO @ Thu, 09 Dec 2021 02:16:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.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 02:16:31: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:16:31: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:16:33: 5000000 INFO @ Thu, 09 Dec 2021 02:16:35: 9000000 INFO @ Thu, 09 Dec 2021 02:16:37: 1000000 INFO @ Thu, 09 Dec 2021 02:16:39: 6000000 INFO @ Thu, 09 Dec 2021 02:16:42: 10000000 INFO @ Thu, 09 Dec 2021 02:16:44: 2000000 INFO @ Thu, 09 Dec 2021 02:16:45: 7000000 INFO @ Thu, 09 Dec 2021 02:16:48: 11000000 INFO @ Thu, 09 Dec 2021 02:16:51: 3000000 INFO @ Thu, 09 Dec 2021 02:16:52: 8000000 INFO @ Thu, 09 Dec 2021 02:16:54: 12000000 INFO @ Thu, 09 Dec 2021 02:16:58: 4000000 INFO @ Thu, 09 Dec 2021 02:16:59: 9000000 INFO @ Thu, 09 Dec 2021 02:17:00: 13000000 INFO @ Thu, 09 Dec 2021 02:17:05: 5000000 INFO @ Thu, 09 Dec 2021 02:17:06: 10000000 INFO @ Thu, 09 Dec 2021 02:17:06: 14000000 INFO @ Thu, 09 Dec 2021 02:17:11: 6000000 INFO @ Thu, 09 Dec 2021 02:17:12: 15000000 INFO @ Thu, 09 Dec 2021 02:17:12: 11000000 INFO @ Thu, 09 Dec 2021 02:17:18: 16000000 INFO @ Thu, 09 Dec 2021 02:17:18: 7000000 INFO @ Thu, 09 Dec 2021 02:17:19: 12000000 INFO @ Thu, 09 Dec 2021 02:17:24: 17000000 INFO @ Thu, 09 Dec 2021 02:17:25: 8000000 INFO @ Thu, 09 Dec 2021 02:17:26: 13000000 INFO @ Thu, 09 Dec 2021 02:17:30: 18000000 INFO @ Thu, 09 Dec 2021 02:17:32: 9000000 INFO @ Thu, 09 Dec 2021 02:17:33: 14000000 INFO @ Thu, 09 Dec 2021 02:17:36: 19000000 INFO @ Thu, 09 Dec 2021 02:17:38: 10000000 INFO @ Thu, 09 Dec 2021 02:17:40: 15000000 INFO @ Thu, 09 Dec 2021 02:17:42: 20000000 INFO @ Thu, 09 Dec 2021 02:17:44: 11000000 INFO @ Thu, 09 Dec 2021 02:17:47: 16000000 INFO @ Thu, 09 Dec 2021 02:17:48: 21000000 INFO @ Thu, 09 Dec 2021 02:17:51: 12000000 INFO @ Thu, 09 Dec 2021 02:17:53: 22000000 INFO @ Thu, 09 Dec 2021 02:17:54: 17000000 INFO @ Thu, 09 Dec 2021 02:17:58: 13000000 INFO @ Thu, 09 Dec 2021 02:17:59: 23000000 INFO @ Thu, 09 Dec 2021 02:18:01: 18000000 INFO @ Thu, 09 Dec 2021 02:18:05: 14000000 INFO @ Thu, 09 Dec 2021 02:18:05: 24000000 INFO @ Thu, 09 Dec 2021 02:18:07: 19000000 INFO @ Thu, 09 Dec 2021 02:18:11: 15000000 INFO @ Thu, 09 Dec 2021 02:18:11: 25000000 INFO @ Thu, 09 Dec 2021 02:18:14: 20000000 INFO @ Thu, 09 Dec 2021 02:18:18: 16000000 INFO @ Thu, 09 Dec 2021 02:18:18: 26000000 INFO @ Thu, 09 Dec 2021 02:18:21: 21000000 INFO @ Thu, 09 Dec 2021 02:18:24: 17000000 INFO @ Thu, 09 Dec 2021 02:18:25: 27000000 INFO @ Thu, 09 Dec 2021 02:18:28: 22000000 INFO @ Thu, 09 Dec 2021 02:18:31: 18000000 INFO @ Thu, 09 Dec 2021 02:18:31: 28000000 INFO @ Thu, 09 Dec 2021 02:18:35: 23000000 INFO @ Thu, 09 Dec 2021 02:18:38: 19000000 INFO @ Thu, 09 Dec 2021 02:18:39: 29000000 INFO @ Thu, 09 Dec 2021 02:18:41: 24000000 INFO @ Thu, 09 Dec 2021 02:18:44: 20000000 INFO @ Thu, 09 Dec 2021 02:18:45: 30000000 INFO @ Thu, 09 Dec 2021 02:18:48: 25000000 INFO @ Thu, 09 Dec 2021 02:18:51: 21000000 INFO @ Thu, 09 Dec 2021 02:18:52: 31000000 INFO @ Thu, 09 Dec 2021 02:18:54: 26000000 INFO @ Thu, 09 Dec 2021 02:18:58: 22000000 INFO @ Thu, 09 Dec 2021 02:18:59: 32000000 INFO @ Thu, 09 Dec 2021 02:19:01: 27000000 INFO @ Thu, 09 Dec 2021 02:19:04: 23000000 INFO @ Thu, 09 Dec 2021 02:19:06: 33000000 INFO @ Thu, 09 Dec 2021 02:19:07: 28000000 INFO @ Thu, 09 Dec 2021 02:19:11: 24000000 INFO @ Thu, 09 Dec 2021 02:19:14: 29000000 INFO @ Thu, 09 Dec 2021 02:19:15: 34000000 INFO @ Thu, 09 Dec 2021 02:19:18: 25000000 INFO @ Thu, 09 Dec 2021 02:19:20: 30000000 INFO @ Thu, 09 Dec 2021 02:19:21: 35000000 INFO @ Thu, 09 Dec 2021 02:19:25: 26000000 INFO @ Thu, 09 Dec 2021 02:19:27: 31000000 INFO @ Thu, 09 Dec 2021 02:19:27: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:19:27: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:19:27: #1 total tags in treatment: 17698642 INFO @ Thu, 09 Dec 2021 02:19:27: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:19:27: #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 02:19:28: #1 tags after filtering in treatment: 15940093 INFO @ Thu, 09 Dec 2021 02:19:28: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 02:19:28: #1 finished! INFO @ Thu, 09 Dec 2021 02:19:28: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:19:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:19:29: #2 number of paired peaks: 349 WARNING @ Thu, 09 Dec 2021 02:19:29: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Thu, 09 Dec 2021 02:19:29: start model_add_line... INFO @ Thu, 09 Dec 2021 02:19:29: start X-correlation... INFO @ Thu, 09 Dec 2021 02:19:29: end of X-cor INFO @ Thu, 09 Dec 2021 02:19:29: #2 finished! INFO @ Thu, 09 Dec 2021 02:19:29: #2 predicted fragment length is 117 bps INFO @ Thu, 09 Dec 2021 02:19:29: #2 alternative fragment length(s) may be 4,117,137 bps INFO @ Thu, 09 Dec 2021 02:19:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.05_model.r INFO @ Thu, 09 Dec 2021 02:19:29: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:19:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:19:31: 27000000 INFO @ Thu, 09 Dec 2021 02:19:34: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:19:38: 28000000 INFO @ Thu, 09 Dec 2021 02:19:40: 33000000 INFO @ Thu, 09 Dec 2021 02:19:45: 29000000 INFO @ Thu, 09 Dec 2021 02:19:47: 34000000 INFO @ Thu, 09 Dec 2021 02:19:51: 30000000 INFO @ Thu, 09 Dec 2021 02:19:53: 35000000 INFO @ Thu, 09 Dec 2021 02:19:57: 31000000 INFO @ Thu, 09 Dec 2021 02:19:58: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:19:58: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:19:58: #1 total tags in treatment: 17698642 INFO @ Thu, 09 Dec 2021 02:19:58: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:19:58: #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 02:19:58: #1 tags after filtering in treatment: 15940093 INFO @ Thu, 09 Dec 2021 02:19:58: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 02:19:58: #1 finished! INFO @ Thu, 09 Dec 2021 02:19:58: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:19:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:19:59: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:19:59: #2 number of paired peaks: 349 WARNING @ Thu, 09 Dec 2021 02:19:59: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Thu, 09 Dec 2021 02:19:59: start model_add_line... INFO @ Thu, 09 Dec 2021 02:19:59: start X-correlation... INFO @ Thu, 09 Dec 2021 02:20:00: end of X-cor INFO @ Thu, 09 Dec 2021 02:20:00: #2 finished! INFO @ Thu, 09 Dec 2021 02:20:00: #2 predicted fragment length is 117 bps INFO @ Thu, 09 Dec 2021 02:20:00: #2 alternative fragment length(s) may be 4,117,137 bps INFO @ Thu, 09 Dec 2021 02:20:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.10_model.r INFO @ Thu, 09 Dec 2021 02:20:00: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:20:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:20:03: 32000000 INFO @ Thu, 09 Dec 2021 02:20:09: 33000000 INFO @ Thu, 09 Dec 2021 02:20:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:20:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:20:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.05_summits.bed INFO @ Thu, 09 Dec 2021 02:20:15: Done! INFO @ Thu, 09 Dec 2021 02:20:15: 34000000 pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (1372 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:20:21: 35000000 INFO @ Thu, 09 Dec 2021 02:20:25: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:20:25: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:20:25: #1 total tags in treatment: 17698642 INFO @ Thu, 09 Dec 2021 02:20:25: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:20:25: #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 02:20:26: #1 tags after filtering in treatment: 15940093 INFO @ Thu, 09 Dec 2021 02:20:26: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 02:20:26: #1 finished! INFO @ Thu, 09 Dec 2021 02:20:26: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:20:27: #2 number of paired peaks: 349 WARNING @ Thu, 09 Dec 2021 02:20:27: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Thu, 09 Dec 2021 02:20:27: start model_add_line... INFO @ Thu, 09 Dec 2021 02:20:27: start X-correlation... INFO @ Thu, 09 Dec 2021 02:20:27: end of X-cor INFO @ Thu, 09 Dec 2021 02:20:27: #2 finished! INFO @ Thu, 09 Dec 2021 02:20:27: #2 predicted fragment length is 117 bps INFO @ Thu, 09 Dec 2021 02:20:27: #2 alternative fragment length(s) may be 4,117,137 bps INFO @ Thu, 09 Dec 2021 02:20:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.20_model.r INFO @ Thu, 09 Dec 2021 02:20:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:20:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:20:30: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:20:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:20:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:20:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.10_summits.bed INFO @ Thu, 09 Dec 2021 02:20:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (693 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:20:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:21:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:21:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:21:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555460/SRX9555460.20_summits.bed INFO @ Thu, 09 Dec 2021 02:21:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (338 records, 4 fields): 2 millis CompletedMACS2peakCalling