Job ID = 14158248 SRX = SRX10342578 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6612031 spots for SRR13964612/SRR13964612.sra Written 6612031 spots for SRR13964612/SRR13964612.sra Read 7291144 spots for SRR13964613/SRR13964613.sra Written 7291144 spots for SRR13964613/SRR13964613.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158670 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:27 13903175 reads; of these: 13903175 (100.00%) were paired; of these: 4063790 (29.23%) aligned concordantly 0 times 8328419 (59.90%) aligned concordantly exactly 1 time 1510966 (10.87%) aligned concordantly >1 times ---- 4063790 pairs aligned concordantly 0 times; of these: 3135336 (77.15%) aligned discordantly 1 time ---- 928454 pairs aligned 0 times concordantly or discordantly; of these: 1856908 mates make up the pairs; of these: 591219 (31.84%) aligned 0 times 498176 (26.83%) aligned exactly 1 time 767513 (41.33%) aligned >1 times 97.87% overall alignment rate Time searching: 00:10:28 Overall time: 00:10:28 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] 938917 / 12963438 = 0.0724 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 @ Wed, 08 Dec 2021 15:18:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.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 @ Wed, 08 Dec 2021 15:18:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:18:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:18:27: 1000000 INFO @ Wed, 08 Dec 2021 15:18:31: 2000000 INFO @ Wed, 08 Dec 2021 15:18:35: 3000000 INFO @ Wed, 08 Dec 2021 15:18:39: 4000000 INFO @ Wed, 08 Dec 2021 15:18:43: 5000000 INFO @ Wed, 08 Dec 2021 15:18:46: 6000000 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 @ Wed, 08 Dec 2021 15:18:50: 7000000 INFO @ Wed, 08 Dec 2021 15:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.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 @ Wed, 08 Dec 2021 15:18:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:18:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:18:55: 8000000 INFO @ Wed, 08 Dec 2021 15:18:56: 1000000 INFO @ Wed, 08 Dec 2021 15:18:59: 9000000 INFO @ Wed, 08 Dec 2021 15:19:00: 2000000 INFO @ Wed, 08 Dec 2021 15:19:03: 10000000 INFO @ Wed, 08 Dec 2021 15:19:04: 3000000 INFO @ Wed, 08 Dec 2021 15:19:07: 11000000 INFO @ Wed, 08 Dec 2021 15:19:08: 4000000 INFO @ Wed, 08 Dec 2021 15:19:11: 12000000 INFO @ Wed, 08 Dec 2021 15:19:12: 5000000 INFO @ Wed, 08 Dec 2021 15:19:15: 13000000 INFO @ Wed, 08 Dec 2021 15:19:16: 6000000 INFO @ Wed, 08 Dec 2021 15:19:19: 14000000 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 @ Wed, 08 Dec 2021 15:19:20: 7000000 INFO @ Wed, 08 Dec 2021 15:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.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 @ Wed, 08 Dec 2021 15:19:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:19:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:19:23: 15000000 INFO @ Wed, 08 Dec 2021 15:19:25: 8000000 INFO @ Wed, 08 Dec 2021 15:19:26: 1000000 INFO @ Wed, 08 Dec 2021 15:19:27: 16000000 INFO @ Wed, 08 Dec 2021 15:19:29: 9000000 INFO @ Wed, 08 Dec 2021 15:19:30: 2000000 INFO @ Wed, 08 Dec 2021 15:19:31: 17000000 INFO @ Wed, 08 Dec 2021 15:19:33: 10000000 INFO @ Wed, 08 Dec 2021 15:19:34: 3000000 INFO @ Wed, 08 Dec 2021 15:19:36: 18000000 INFO @ Wed, 08 Dec 2021 15:19:37: 11000000 INFO @ Wed, 08 Dec 2021 15:19:38: 4000000 INFO @ Wed, 08 Dec 2021 15:19:40: 19000000 INFO @ Wed, 08 Dec 2021 15:19:41: 12000000 INFO @ Wed, 08 Dec 2021 15:19:42: 5000000 INFO @ Wed, 08 Dec 2021 15:19:44: 20000000 INFO @ Wed, 08 Dec 2021 15:19:45: 13000000 INFO @ Wed, 08 Dec 2021 15:19:47: 6000000 INFO @ Wed, 08 Dec 2021 15:19:48: 21000000 INFO @ Wed, 08 Dec 2021 15:19:49: 14000000 INFO @ Wed, 08 Dec 2021 15:19:51: 7000000 INFO @ Wed, 08 Dec 2021 15:19:52: 22000000 INFO @ Wed, 08 Dec 2021 15:19:53: 15000000 INFO @ Wed, 08 Dec 2021 15:19:55: 8000000 INFO @ Wed, 08 Dec 2021 15:19:56: 23000000 INFO @ Wed, 08 Dec 2021 15:19:57: 16000000 INFO @ Wed, 08 Dec 2021 15:19:59: 9000000 INFO @ Wed, 08 Dec 2021 15:20:00: 24000000 INFO @ Wed, 08 Dec 2021 15:20:02: 17000000 INFO @ Wed, 08 Dec 2021 15:20:03: 10000000 INFO @ Wed, 08 Dec 2021 15:20:04: 25000000 INFO @ Wed, 08 Dec 2021 15:20:06: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:20:06: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:20:06: #1 total tags in treatment: 9082565 INFO @ Wed, 08 Dec 2021 15:20:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:20:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:20:06: 18000000 INFO @ Wed, 08 Dec 2021 15:20:06: #1 tags after filtering in treatment: 8375441 INFO @ Wed, 08 Dec 2021 15:20:06: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 15:20:06: #1 finished! INFO @ Wed, 08 Dec 2021 15:20:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:20:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:20:06: #2 number of paired peaks: 518 WARNING @ Wed, 08 Dec 2021 15:20:06: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Wed, 08 Dec 2021 15:20:06: start model_add_line... INFO @ Wed, 08 Dec 2021 15:20:06: start X-correlation... INFO @ Wed, 08 Dec 2021 15:20:06: end of X-cor INFO @ Wed, 08 Dec 2021 15:20:06: #2 finished! INFO @ Wed, 08 Dec 2021 15:20:06: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 15:20:06: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 15:20:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.05_model.r INFO @ Wed, 08 Dec 2021 15:20:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:20:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:20:07: 11000000 INFO @ Wed, 08 Dec 2021 15:20:10: 19000000 INFO @ Wed, 08 Dec 2021 15:20:11: 12000000 INFO @ Wed, 08 Dec 2021 15:20:14: 20000000 INFO @ Wed, 08 Dec 2021 15:20:16: 13000000 INFO @ Wed, 08 Dec 2021 15:20:18: 21000000 INFO @ Wed, 08 Dec 2021 15:20:20: 14000000 INFO @ Wed, 08 Dec 2021 15:20:22: 22000000 INFO @ Wed, 08 Dec 2021 15:20:24: 15000000 INFO @ Wed, 08 Dec 2021 15:20:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:20:26: 23000000 INFO @ Wed, 08 Dec 2021 15:20:28: 16000000 INFO @ Wed, 08 Dec 2021 15:20:30: 24000000 INFO @ Wed, 08 Dec 2021 15:20:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:20:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:20:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.05_summits.bed INFO @ Wed, 08 Dec 2021 15:20:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (393 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:20:32: 17000000 INFO @ Wed, 08 Dec 2021 15:20:34: 25000000 INFO @ Wed, 08 Dec 2021 15:20:36: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:20:36: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:20:36: #1 total tags in treatment: 9082565 INFO @ Wed, 08 Dec 2021 15:20:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:20:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:20:36: #1 tags after filtering in treatment: 8375441 INFO @ Wed, 08 Dec 2021 15:20:36: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 15:20:36: #1 finished! INFO @ Wed, 08 Dec 2021 15:20:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:20:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:20:36: 18000000 INFO @ Wed, 08 Dec 2021 15:20:36: #2 number of paired peaks: 518 WARNING @ Wed, 08 Dec 2021 15:20:36: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Wed, 08 Dec 2021 15:20:36: start model_add_line... INFO @ Wed, 08 Dec 2021 15:20:36: start X-correlation... INFO @ Wed, 08 Dec 2021 15:20:36: end of X-cor INFO @ Wed, 08 Dec 2021 15:20:36: #2 finished! INFO @ Wed, 08 Dec 2021 15:20:36: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 15:20:36: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 15:20:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.10_model.r INFO @ Wed, 08 Dec 2021 15:20:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:20:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:20:40: 19000000 INFO @ Wed, 08 Dec 2021 15:20:44: 20000000 INFO @ Wed, 08 Dec 2021 15:20:48: 21000000 INFO @ Wed, 08 Dec 2021 15:20:52: 22000000 INFO @ Wed, 08 Dec 2021 15:20:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:20:56: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:20:59: 24000000 INFO @ Wed, 08 Dec 2021 15:21:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:21:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:21:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.10_summits.bed INFO @ Wed, 08 Dec 2021 15:21:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (296 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:21:03: 25000000 INFO @ Wed, 08 Dec 2021 15:21:05: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:21:05: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:21:05: #1 total tags in treatment: 9082565 INFO @ Wed, 08 Dec 2021 15:21:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:21:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:21:05: #1 tags after filtering in treatment: 8375441 INFO @ Wed, 08 Dec 2021 15:21:05: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 15:21:05: #1 finished! INFO @ Wed, 08 Dec 2021 15:21:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:21:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:21:05: #2 number of paired peaks: 518 WARNING @ Wed, 08 Dec 2021 15:21:06: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Wed, 08 Dec 2021 15:21:06: start model_add_line... INFO @ Wed, 08 Dec 2021 15:21:06: start X-correlation... INFO @ Wed, 08 Dec 2021 15:21:06: end of X-cor INFO @ Wed, 08 Dec 2021 15:21:06: #2 finished! INFO @ Wed, 08 Dec 2021 15:21:06: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 15:21:06: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 15:21:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.20_model.r INFO @ Wed, 08 Dec 2021 15:21:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:21:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:21:23: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:21:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:21:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:21:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342578/SRX10342578.20_summits.bed INFO @ Wed, 08 Dec 2021 15:21:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (197 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。