Job ID = 14158501 SRX = SRX8976703 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12237385 spots for SRR12483307/SRR12483307.sra Written 12237385 spots for SRR12483307/SRR12483307.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159141 ("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: 00:10:17 12237385 reads; of these: 12237385 (100.00%) were paired; of these: 987039 (8.07%) aligned concordantly 0 times 9745700 (79.64%) aligned concordantly exactly 1 time 1504646 (12.30%) aligned concordantly >1 times ---- 987039 pairs aligned concordantly 0 times; of these: 694902 (70.40%) aligned discordantly 1 time ---- 292137 pairs aligned 0 times concordantly or discordantly; of these: 584274 mates make up the pairs; of these: 245764 (42.06%) aligned 0 times 156832 (26.84%) aligned exactly 1 time 181678 (31.09%) aligned >1 times 99.00% overall alignment rate Time searching: 00:10:17 Overall time: 00:10:17 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 12 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] 201736 / 11934756 = 0.0169 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 17:57:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.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 17:57:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:57:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:57:32: 1000000 INFO @ Wed, 08 Dec 2021 17:57:38: 2000000 INFO @ Wed, 08 Dec 2021 17:57:44: 3000000 INFO @ Wed, 08 Dec 2021 17:57:50: 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 @ Wed, 08 Dec 2021 17:57:56: 5000000 INFO @ Wed, 08 Dec 2021 17:57:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.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 17:57:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:57:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:58:02: 6000000 INFO @ Wed, 08 Dec 2021 17:58:02: 1000000 INFO @ Wed, 08 Dec 2021 17:58:08: 7000000 INFO @ Wed, 08 Dec 2021 17:58:08: 2000000 INFO @ Wed, 08 Dec 2021 17:58:15: 8000000 INFO @ Wed, 08 Dec 2021 17:58:15: 3000000 INFO @ Wed, 08 Dec 2021 17:58:21: 9000000 INFO @ Wed, 08 Dec 2021 17:58:21: 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 @ Wed, 08 Dec 2021 17:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.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 17:58:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:58:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:58:27: 10000000 INFO @ Wed, 08 Dec 2021 17:58:28: 5000000 INFO @ Wed, 08 Dec 2021 17:58:32: 1000000 INFO @ Wed, 08 Dec 2021 17:58:34: 11000000 INFO @ Wed, 08 Dec 2021 17:58:34: 6000000 INFO @ Wed, 08 Dec 2021 17:58:38: 2000000 INFO @ Wed, 08 Dec 2021 17:58:40: 12000000 INFO @ Wed, 08 Dec 2021 17:58:41: 7000000 INFO @ Wed, 08 Dec 2021 17:58:44: 3000000 INFO @ Wed, 08 Dec 2021 17:58:47: 13000000 INFO @ Wed, 08 Dec 2021 17:58:47: 8000000 INFO @ Wed, 08 Dec 2021 17:58:51: 4000000 INFO @ Wed, 08 Dec 2021 17:58:53: 14000000 INFO @ Wed, 08 Dec 2021 17:58:54: 9000000 INFO @ Wed, 08 Dec 2021 17:58:57: 5000000 INFO @ Wed, 08 Dec 2021 17:59:00: 15000000 INFO @ Wed, 08 Dec 2021 17:59:00: 10000000 INFO @ Wed, 08 Dec 2021 17:59:04: 6000000 INFO @ Wed, 08 Dec 2021 17:59:06: 16000000 INFO @ Wed, 08 Dec 2021 17:59:07: 11000000 INFO @ Wed, 08 Dec 2021 17:59:10: 7000000 INFO @ Wed, 08 Dec 2021 17:59:13: 17000000 INFO @ Wed, 08 Dec 2021 17:59:14: 12000000 INFO @ Wed, 08 Dec 2021 17:59:17: 8000000 INFO @ Wed, 08 Dec 2021 17:59:19: 18000000 INFO @ Wed, 08 Dec 2021 17:59:20: 13000000 INFO @ Wed, 08 Dec 2021 17:59:23: 9000000 INFO @ Wed, 08 Dec 2021 17:59:26: 19000000 INFO @ Wed, 08 Dec 2021 17:59:27: 14000000 INFO @ Wed, 08 Dec 2021 17:59:30: 10000000 INFO @ Wed, 08 Dec 2021 17:59:32: 20000000 INFO @ Wed, 08 Dec 2021 17:59:33: 15000000 INFO @ Wed, 08 Dec 2021 17:59:36: 11000000 INFO @ Wed, 08 Dec 2021 17:59:38: 21000000 INFO @ Wed, 08 Dec 2021 17:59:40: 16000000 INFO @ Wed, 08 Dec 2021 17:59:43: 12000000 INFO @ Wed, 08 Dec 2021 17:59:45: 22000000 INFO @ Wed, 08 Dec 2021 17:59:46: 17000000 INFO @ Wed, 08 Dec 2021 17:59:49: 13000000 INFO @ Wed, 08 Dec 2021 17:59:51: 23000000 INFO @ Wed, 08 Dec 2021 17:59:53: 18000000 INFO @ Wed, 08 Dec 2021 17:59:55: 14000000 INFO @ Wed, 08 Dec 2021 17:59:56: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 17:59:56: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 17:59:56: #1 total tags in treatment: 11056157 INFO @ Wed, 08 Dec 2021 17:59:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:59:56: #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 17:59:57: #1 tags after filtering in treatment: 10392736 INFO @ Wed, 08 Dec 2021 17:59:57: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 17:59:57: #1 finished! INFO @ Wed, 08 Dec 2021 17:59:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:59:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:59:57: #2 number of paired peaks: 363 WARNING @ Wed, 08 Dec 2021 17:59:57: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Wed, 08 Dec 2021 17:59:57: start model_add_line... INFO @ Wed, 08 Dec 2021 17:59:57: start X-correlation... INFO @ Wed, 08 Dec 2021 17:59:57: end of X-cor INFO @ Wed, 08 Dec 2021 17:59:57: #2 finished! INFO @ Wed, 08 Dec 2021 17:59:57: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 17:59:57: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 17:59:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.05_model.r INFO @ Wed, 08 Dec 2021 17:59:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:59:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:59:59: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:00:02: 15000000 INFO @ Wed, 08 Dec 2021 18:00:05: 20000000 INFO @ Wed, 08 Dec 2021 18:00:08: 16000000 INFO @ Wed, 08 Dec 2021 18:00:11: 21000000 INFO @ Wed, 08 Dec 2021 18:00:14: 17000000 INFO @ Wed, 08 Dec 2021 18:00:18: 22000000 INFO @ Wed, 08 Dec 2021 18:00:18: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:00:21: 18000000 INFO @ Wed, 08 Dec 2021 18:00:24: 23000000 INFO @ Wed, 08 Dec 2021 18:00:27: 19000000 INFO @ Wed, 08 Dec 2021 18:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:00:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.05_summits.bed INFO @ Wed, 08 Dec 2021 18:00:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:00:29: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:00:29: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:00:29: #1 total tags in treatment: 11056157 INFO @ Wed, 08 Dec 2021 18:00:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:00:29: #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 18:00:29: #1 tags after filtering in treatment: 10392736 INFO @ Wed, 08 Dec 2021 18:00:29: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:00:29: #1 finished! INFO @ Wed, 08 Dec 2021 18:00:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:00:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:00:30: #2 number of paired peaks: 363 WARNING @ Wed, 08 Dec 2021 18:00:30: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Wed, 08 Dec 2021 18:00:30: start model_add_line... INFO @ Wed, 08 Dec 2021 18:00:30: start X-correlation... INFO @ Wed, 08 Dec 2021 18:00:30: end of X-cor INFO @ Wed, 08 Dec 2021 18:00:30: #2 finished! INFO @ Wed, 08 Dec 2021 18:00:30: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 18:00:30: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 18:00:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.10_model.r INFO @ Wed, 08 Dec 2021 18:00:30: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:00:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:00:33: 20000000 INFO @ Wed, 08 Dec 2021 18:00:39: 21000000 INFO @ Wed, 08 Dec 2021 18:00:45: 22000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:00:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:00:51: 23000000 INFO @ Wed, 08 Dec 2021 18:00:56: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:00:56: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:00:56: #1 total tags in treatment: 11056157 INFO @ Wed, 08 Dec 2021 18:00:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:00:56: #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 18:00:56: #1 tags after filtering in treatment: 10392736 INFO @ Wed, 08 Dec 2021 18:00:56: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:00:56: #1 finished! INFO @ Wed, 08 Dec 2021 18:00:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:00:56: #2 number of paired peaks: 363 WARNING @ Wed, 08 Dec 2021 18:00:56: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Wed, 08 Dec 2021 18:00:56: start model_add_line... INFO @ Wed, 08 Dec 2021 18:00:57: start X-correlation... INFO @ Wed, 08 Dec 2021 18:00:57: end of X-cor INFO @ Wed, 08 Dec 2021 18:00:57: #2 finished! INFO @ Wed, 08 Dec 2021 18:00:57: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 18:00:57: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 18:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.20_model.r INFO @ Wed, 08 Dec 2021 18:00:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:00:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:00:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:00:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.10_summits.bed INFO @ Wed, 08 Dec 2021 18:00:59: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (257 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:01:17: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:01:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:01:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:01:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976703/SRX8976703.20_summits.bed INFO @ Wed, 08 Dec 2021 18:01:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (188 records, 4 fields): 2 millis CompletedMACS2peakCalling