Job ID = 14159084 SRX = SRX8976732 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14824795 spots for SRR12483276/SRR12483276.sra Written 14824795 spots for SRR12483276/SRR12483276.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159320 ("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: 00:11:19 14824795 reads; of these: 14824795 (100.00%) were paired; of these: 773357 (5.22%) aligned concordantly 0 times 12240457 (82.57%) aligned concordantly exactly 1 time 1810981 (12.22%) aligned concordantly >1 times ---- 773357 pairs aligned concordantly 0 times; of these: 525173 (67.91%) aligned discordantly 1 time ---- 248184 pairs aligned 0 times concordantly or discordantly; of these: 496368 mates make up the pairs; of these: 175932 (35.44%) aligned 0 times 161961 (32.63%) aligned exactly 1 time 158475 (31.93%) aligned >1 times 99.41% overall alignment rate Time searching: 00:11:19 Overall time: 00:11:19 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] 446068 / 14541302 = 0.0307 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 19:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.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 19:10:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:10:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:10:25: 1000000 INFO @ Wed, 08 Dec 2021 19:10:30: 2000000 INFO @ Wed, 08 Dec 2021 19:10:35: 3000000 INFO @ Wed, 08 Dec 2021 19:10:40: 4000000 INFO @ Wed, 08 Dec 2021 19:10:45: 5000000 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 19:10:50: 6000000 INFO @ Wed, 08 Dec 2021 19:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.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 19:10:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:10:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:10:55: 7000000 INFO @ Wed, 08 Dec 2021 19:10:55: 1000000 INFO @ Wed, 08 Dec 2021 19:11:00: 8000000 INFO @ Wed, 08 Dec 2021 19:11:01: 2000000 INFO @ Wed, 08 Dec 2021 19:11:05: 9000000 INFO @ Wed, 08 Dec 2021 19:11:06: 3000000 INFO @ Wed, 08 Dec 2021 19:11:10: 10000000 INFO @ Wed, 08 Dec 2021 19:11:12: 4000000 INFO @ Wed, 08 Dec 2021 19:11:15: 11000000 INFO @ Wed, 08 Dec 2021 19:11:17: 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 @ Wed, 08 Dec 2021 19:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.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 19:11:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:11:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:11:20: 12000000 INFO @ Wed, 08 Dec 2021 19:11:23: 6000000 INFO @ Wed, 08 Dec 2021 19:11:25: 1000000 INFO @ Wed, 08 Dec 2021 19:11:25: 13000000 INFO @ Wed, 08 Dec 2021 19:11:27: 7000000 INFO @ Wed, 08 Dec 2021 19:11:30: 2000000 INFO @ Wed, 08 Dec 2021 19:11:30: 14000000 INFO @ Wed, 08 Dec 2021 19:11:32: 8000000 INFO @ Wed, 08 Dec 2021 19:11:35: 3000000 INFO @ Wed, 08 Dec 2021 19:11:35: 15000000 INFO @ Wed, 08 Dec 2021 19:11:37: 9000000 INFO @ Wed, 08 Dec 2021 19:11:40: 16000000 INFO @ Wed, 08 Dec 2021 19:11:41: 4000000 INFO @ Wed, 08 Dec 2021 19:11:43: 10000000 INFO @ Wed, 08 Dec 2021 19:11:45: 17000000 INFO @ Wed, 08 Dec 2021 19:11:46: 5000000 INFO @ Wed, 08 Dec 2021 19:11:48: 11000000 INFO @ Wed, 08 Dec 2021 19:11:50: 18000000 INFO @ Wed, 08 Dec 2021 19:11:51: 6000000 INFO @ Wed, 08 Dec 2021 19:11:53: 12000000 INFO @ Wed, 08 Dec 2021 19:11:55: 19000000 INFO @ Wed, 08 Dec 2021 19:11:56: 7000000 INFO @ Wed, 08 Dec 2021 19:11:58: 13000000 INFO @ Wed, 08 Dec 2021 19:12:00: 20000000 INFO @ Wed, 08 Dec 2021 19:12:01: 8000000 INFO @ Wed, 08 Dec 2021 19:12:04: 14000000 INFO @ Wed, 08 Dec 2021 19:12:05: 21000000 INFO @ Wed, 08 Dec 2021 19:12:06: 9000000 INFO @ Wed, 08 Dec 2021 19:12:08: 15000000 INFO @ Wed, 08 Dec 2021 19:12:10: 22000000 INFO @ Wed, 08 Dec 2021 19:12:11: 10000000 INFO @ Wed, 08 Dec 2021 19:12:13: 16000000 INFO @ Wed, 08 Dec 2021 19:12:15: 23000000 INFO @ Wed, 08 Dec 2021 19:12:16: 11000000 INFO @ Wed, 08 Dec 2021 19:12:18: 17000000 INFO @ Wed, 08 Dec 2021 19:12:20: 24000000 INFO @ Wed, 08 Dec 2021 19:12:22: 12000000 INFO @ Wed, 08 Dec 2021 19:12:24: 18000000 INFO @ Wed, 08 Dec 2021 19:12:25: 25000000 INFO @ Wed, 08 Dec 2021 19:12:27: 13000000 INFO @ Wed, 08 Dec 2021 19:12:29: 19000000 INFO @ Wed, 08 Dec 2021 19:12:30: 26000000 INFO @ Wed, 08 Dec 2021 19:12:32: 14000000 INFO @ Wed, 08 Dec 2021 19:12:34: 20000000 INFO @ Wed, 08 Dec 2021 19:12:35: 27000000 INFO @ Wed, 08 Dec 2021 19:12:37: 15000000 INFO @ Wed, 08 Dec 2021 19:12:39: 21000000 INFO @ Wed, 08 Dec 2021 19:12:40: 28000000 INFO @ Wed, 08 Dec 2021 19:12:42: 16000000 INFO @ Wed, 08 Dec 2021 19:12:43: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:12:43: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:12:43: #1 total tags in treatment: 13617081 INFO @ Wed, 08 Dec 2021 19:12:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:12:43: #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 19:12:44: #1 tags after filtering in treatment: 12671277 INFO @ Wed, 08 Dec 2021 19:12:44: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:12:44: #1 finished! INFO @ Wed, 08 Dec 2021 19:12:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:12:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:12:44: 22000000 INFO @ Wed, 08 Dec 2021 19:12:44: #2 number of paired peaks: 294 WARNING @ Wed, 08 Dec 2021 19:12:44: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Wed, 08 Dec 2021 19:12:44: start model_add_line... INFO @ Wed, 08 Dec 2021 19:12:44: start X-correlation... INFO @ Wed, 08 Dec 2021 19:12:44: end of X-cor INFO @ Wed, 08 Dec 2021 19:12:44: #2 finished! INFO @ Wed, 08 Dec 2021 19:12:44: #2 predicted fragment length is 152 bps INFO @ Wed, 08 Dec 2021 19:12:44: #2 alternative fragment length(s) may be 4,152 bps INFO @ Wed, 08 Dec 2021 19:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.05_model.r INFO @ Wed, 08 Dec 2021 19:12:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:12:46: 17000000 INFO @ Wed, 08 Dec 2021 19:12:49: 23000000 INFO @ Wed, 08 Dec 2021 19:12:51: 18000000 INFO @ Wed, 08 Dec 2021 19:12:55: 24000000 INFO @ Wed, 08 Dec 2021 19:12:56: 19000000 INFO @ Wed, 08 Dec 2021 19:13:00: 25000000 INFO @ Wed, 08 Dec 2021 19:13:01: 20000000 INFO @ Wed, 08 Dec 2021 19:13:05: 26000000 INFO @ Wed, 08 Dec 2021 19:13:06: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:13:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:13:10: 27000000 INFO @ Wed, 08 Dec 2021 19:13:11: 22000000 INFO @ Wed, 08 Dec 2021 19:13:15: 28000000 INFO @ Wed, 08 Dec 2021 19:13:16: 23000000 INFO @ Wed, 08 Dec 2021 19:13:18: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:13:18: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:13:18: #1 total tags in treatment: 13617081 INFO @ Wed, 08 Dec 2021 19:13:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:13:18: #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 19:13:18: #1 tags after filtering in treatment: 12671277 INFO @ Wed, 08 Dec 2021 19:13:18: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:13:18: #1 finished! INFO @ Wed, 08 Dec 2021 19:13:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:13:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:13:19: #2 number of paired peaks: 294 WARNING @ Wed, 08 Dec 2021 19:13:19: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Wed, 08 Dec 2021 19:13:19: start model_add_line... INFO @ Wed, 08 Dec 2021 19:13:19: start X-correlation... INFO @ Wed, 08 Dec 2021 19:13:19: end of X-cor INFO @ Wed, 08 Dec 2021 19:13:19: #2 finished! INFO @ Wed, 08 Dec 2021 19:13:19: #2 predicted fragment length is 152 bps INFO @ Wed, 08 Dec 2021 19:13:19: #2 alternative fragment length(s) may be 4,152 bps INFO @ Wed, 08 Dec 2021 19:13:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.10_model.r INFO @ Wed, 08 Dec 2021 19:13:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:13:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:13:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:13:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:13:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.05_summits.bed INFO @ Wed, 08 Dec 2021 19:13:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (350 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:13:21: 24000000 INFO @ Wed, 08 Dec 2021 19:13:26: 25000000 INFO @ Wed, 08 Dec 2021 19:13:31: 26000000 INFO @ Wed, 08 Dec 2021 19:13:35: 27000000 INFO @ Wed, 08 Dec 2021 19:13:40: 28000000 INFO @ Wed, 08 Dec 2021 19:13:43: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:13:43: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:13:43: #1 total tags in treatment: 13617081 INFO @ Wed, 08 Dec 2021 19:13:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:13:43: #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 19:13:43: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:13:43: #1 tags after filtering in treatment: 12671277 INFO @ Wed, 08 Dec 2021 19:13:43: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:13:43: #1 finished! INFO @ Wed, 08 Dec 2021 19:13:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:13:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:13:44: #2 number of paired peaks: 294 WARNING @ Wed, 08 Dec 2021 19:13:44: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Wed, 08 Dec 2021 19:13:44: start model_add_line... INFO @ Wed, 08 Dec 2021 19:13:44: start X-correlation... INFO @ Wed, 08 Dec 2021 19:13:44: end of X-cor INFO @ Wed, 08 Dec 2021 19:13:44: #2 finished! INFO @ Wed, 08 Dec 2021 19:13:44: #2 predicted fragment length is 152 bps INFO @ Wed, 08 Dec 2021 19:13:44: #2 alternative fragment length(s) may be 4,152 bps INFO @ Wed, 08 Dec 2021 19:13:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.20_model.r INFO @ Wed, 08 Dec 2021 19:13:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:13:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:13:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:13:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:13:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.10_summits.bed INFO @ Wed, 08 Dec 2021 19:13:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (246 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:14:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:14:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:14:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:14:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976732/SRX8976732.20_summits.bed INFO @ Wed, 08 Dec 2021 19:14:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (180 records, 4 fields): 2 millis CompletedMACS2peakCalling