Job ID = 14158793 SRX = SRX10342584 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:27 18079315 reads; of these: 18079315 (100.00%) were paired; of these: 1437964 (7.95%) aligned concordantly 0 times 14500331 (80.20%) aligned concordantly exactly 1 time 2141020 (11.84%) aligned concordantly >1 times ---- 1437964 pairs aligned concordantly 0 times; of these: 1023894 (71.20%) aligned discordantly 1 time ---- 414070 pairs aligned 0 times concordantly or discordantly; of these: 828140 mates make up the pairs; of these: 328739 (39.70%) aligned 0 times 217669 (26.28%) aligned exactly 1 time 281732 (34.02%) aligned >1 times 99.09% overall alignment rate Time searching: 00:13:27 Overall time: 00:13:27 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] 881020 / 17630190 = 0.0500 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 18:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.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 18:17:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:17:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:17:05: 1000000 INFO @ Wed, 08 Dec 2021 18:17:10: 2000000 INFO @ Wed, 08 Dec 2021 18:17:15: 3000000 INFO @ Wed, 08 Dec 2021 18:17:19: 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 18:17:24: 5000000 INFO @ Wed, 08 Dec 2021 18:17:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.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 18:17:24: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:17:24: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:17:29: 1000000 INFO @ Wed, 08 Dec 2021 18:17:29: 6000000 INFO @ Wed, 08 Dec 2021 18:17:33: 2000000 INFO @ Wed, 08 Dec 2021 18:17:34: 7000000 INFO @ Wed, 08 Dec 2021 18:17:38: 3000000 INFO @ Wed, 08 Dec 2021 18:17:39: 8000000 INFO @ Wed, 08 Dec 2021 18:17:43: 4000000 INFO @ Wed, 08 Dec 2021 18:17:44: 9000000 INFO @ Wed, 08 Dec 2021 18:17:47: 5000000 INFO @ Wed, 08 Dec 2021 18:17:49: 10000000 INFO @ Wed, 08 Dec 2021 18:17:51: 6000000 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 18:17:54: 11000000 INFO @ Wed, 08 Dec 2021 18:17:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.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 18:17:54: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:17:54: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:17:56: 7000000 INFO @ Wed, 08 Dec 2021 18:17:59: 1000000 INFO @ Wed, 08 Dec 2021 18:17:59: 12000000 INFO @ Wed, 08 Dec 2021 18:18:01: 8000000 INFO @ Wed, 08 Dec 2021 18:18:04: 2000000 INFO @ Wed, 08 Dec 2021 18:18:04: 13000000 INFO @ Wed, 08 Dec 2021 18:18:05: 9000000 INFO @ Wed, 08 Dec 2021 18:18:08: 3000000 INFO @ Wed, 08 Dec 2021 18:18:10: 14000000 INFO @ Wed, 08 Dec 2021 18:18:10: 10000000 INFO @ Wed, 08 Dec 2021 18:18:13: 4000000 INFO @ Wed, 08 Dec 2021 18:18:14: 11000000 INFO @ Wed, 08 Dec 2021 18:18:15: 15000000 INFO @ Wed, 08 Dec 2021 18:18:17: 5000000 INFO @ Wed, 08 Dec 2021 18:18:19: 12000000 INFO @ Wed, 08 Dec 2021 18:18:20: 16000000 INFO @ Wed, 08 Dec 2021 18:18:22: 6000000 INFO @ Wed, 08 Dec 2021 18:18:23: 13000000 INFO @ Wed, 08 Dec 2021 18:18:25: 17000000 INFO @ Wed, 08 Dec 2021 18:18:27: 7000000 INFO @ Wed, 08 Dec 2021 18:18:27: 14000000 INFO @ Wed, 08 Dec 2021 18:18:31: 18000000 INFO @ Wed, 08 Dec 2021 18:18:32: 8000000 INFO @ Wed, 08 Dec 2021 18:18:32: 15000000 INFO @ Wed, 08 Dec 2021 18:18:36: 19000000 INFO @ Wed, 08 Dec 2021 18:18:36: 16000000 INFO @ Wed, 08 Dec 2021 18:18:36: 9000000 INFO @ Wed, 08 Dec 2021 18:18:41: 17000000 INFO @ Wed, 08 Dec 2021 18:18:41: 20000000 INFO @ Wed, 08 Dec 2021 18:18:41: 10000000 INFO @ Wed, 08 Dec 2021 18:18:45: 18000000 INFO @ Wed, 08 Dec 2021 18:18:46: 11000000 INFO @ Wed, 08 Dec 2021 18:18:46: 21000000 INFO @ Wed, 08 Dec 2021 18:18:50: 19000000 INFO @ Wed, 08 Dec 2021 18:18:50: 12000000 INFO @ Wed, 08 Dec 2021 18:18:51: 22000000 INFO @ Wed, 08 Dec 2021 18:18:54: 20000000 INFO @ Wed, 08 Dec 2021 18:18:55: 13000000 INFO @ Wed, 08 Dec 2021 18:18:56: 23000000 INFO @ Wed, 08 Dec 2021 18:18:59: 21000000 INFO @ Wed, 08 Dec 2021 18:18:59: 14000000 INFO @ Wed, 08 Dec 2021 18:19:01: 24000000 INFO @ Wed, 08 Dec 2021 18:19:03: 22000000 INFO @ Wed, 08 Dec 2021 18:19:04: 15000000 INFO @ Wed, 08 Dec 2021 18:19:06: 25000000 INFO @ Wed, 08 Dec 2021 18:19:08: 23000000 INFO @ Wed, 08 Dec 2021 18:19:08: 16000000 INFO @ Wed, 08 Dec 2021 18:19:11: 26000000 INFO @ Wed, 08 Dec 2021 18:19:12: 24000000 INFO @ Wed, 08 Dec 2021 18:19:13: 17000000 INFO @ Wed, 08 Dec 2021 18:19:16: 27000000 INFO @ Wed, 08 Dec 2021 18:19:17: 25000000 INFO @ Wed, 08 Dec 2021 18:19:17: 18000000 INFO @ Wed, 08 Dec 2021 18:19:21: 28000000 INFO @ Wed, 08 Dec 2021 18:19:21: 26000000 INFO @ Wed, 08 Dec 2021 18:19:22: 19000000 INFO @ Wed, 08 Dec 2021 18:19:25: 29000000 INFO @ Wed, 08 Dec 2021 18:19:26: 27000000 INFO @ Wed, 08 Dec 2021 18:19:26: 20000000 INFO @ Wed, 08 Dec 2021 18:19:30: 28000000 INFO @ Wed, 08 Dec 2021 18:19:30: 30000000 INFO @ Wed, 08 Dec 2021 18:19:31: 21000000 INFO @ Wed, 08 Dec 2021 18:19:35: 29000000 INFO @ Wed, 08 Dec 2021 18:19:35: 31000000 INFO @ Wed, 08 Dec 2021 18:19:35: 22000000 INFO @ Wed, 08 Dec 2021 18:19:39: 30000000 INFO @ Wed, 08 Dec 2021 18:19:40: 23000000 INFO @ Wed, 08 Dec 2021 18:19:40: 32000000 INFO @ Wed, 08 Dec 2021 18:19:44: 31000000 INFO @ Wed, 08 Dec 2021 18:19:44: 24000000 INFO @ Wed, 08 Dec 2021 18:19:45: 33000000 INFO @ Wed, 08 Dec 2021 18:19:48: 32000000 INFO @ Wed, 08 Dec 2021 18:19:49: 25000000 INFO @ Wed, 08 Dec 2021 18:19:50: 34000000 INFO @ Wed, 08 Dec 2021 18:19:51: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:19:51: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:19:51: #1 total tags in treatment: 15800392 INFO @ Wed, 08 Dec 2021 18:19:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:19:51: #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 18:19:51: #1 tags after filtering in treatment: 14440131 INFO @ Wed, 08 Dec 2021 18:19:51: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:19:51: #1 finished! INFO @ Wed, 08 Dec 2021 18:19:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:19:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:19:52: #2 number of paired peaks: 317 WARNING @ Wed, 08 Dec 2021 18:19:52: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Wed, 08 Dec 2021 18:19:52: start model_add_line... INFO @ Wed, 08 Dec 2021 18:19:52: start X-correlation... INFO @ Wed, 08 Dec 2021 18:19:52: end of X-cor INFO @ Wed, 08 Dec 2021 18:19:52: #2 finished! INFO @ Wed, 08 Dec 2021 18:19:52: #2 predicted fragment length is 110 bps INFO @ Wed, 08 Dec 2021 18:19:52: #2 alternative fragment length(s) may be 3,110,143 bps INFO @ Wed, 08 Dec 2021 18:19:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.05_model.r INFO @ Wed, 08 Dec 2021 18:19:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:19:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:19:53: 33000000 INFO @ Wed, 08 Dec 2021 18:19:53: 26000000 INFO @ Wed, 08 Dec 2021 18:19:57: 34000000 INFO @ Wed, 08 Dec 2021 18:19:57: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:19:57: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:19:57: #1 total tags in treatment: 15800392 INFO @ Wed, 08 Dec 2021 18:19:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:19:57: #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 18:19:57: #1 tags after filtering in treatment: 14440131 INFO @ Wed, 08 Dec 2021 18:19:57: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:19:57: #1 finished! INFO @ Wed, 08 Dec 2021 18:19:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:19:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:19:58: 27000000 INFO @ Wed, 08 Dec 2021 18:19:58: #2 number of paired peaks: 317 WARNING @ Wed, 08 Dec 2021 18:19:58: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Wed, 08 Dec 2021 18:19:58: start model_add_line... INFO @ Wed, 08 Dec 2021 18:19:58: start X-correlation... INFO @ Wed, 08 Dec 2021 18:19:59: end of X-cor INFO @ Wed, 08 Dec 2021 18:19:59: #2 finished! INFO @ Wed, 08 Dec 2021 18:19:59: #2 predicted fragment length is 110 bps INFO @ Wed, 08 Dec 2021 18:19:59: #2 alternative fragment length(s) may be 3,110,143 bps INFO @ Wed, 08 Dec 2021 18:19:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.10_model.r INFO @ Wed, 08 Dec 2021 18:19:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:19:59: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:20:02: 28000000 INFO @ Wed, 08 Dec 2021 18:20:06: 29000000 INFO @ Wed, 08 Dec 2021 18:20:10: 30000000 INFO @ Wed, 08 Dec 2021 18:20:14: 31000000 INFO @ Wed, 08 Dec 2021 18:20:18: 32000000 INFO @ Wed, 08 Dec 2021 18:20:19: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:20:22: 33000000 INFO @ Wed, 08 Dec 2021 18:20:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:20:50: 34000000 INFO @ Wed, 08 Dec 2021 18:20:51: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:20:51: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:20:51: #1 total tags in treatment: 15800392 INFO @ Wed, 08 Dec 2021 18:20:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:20:51: #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 18:20:51: #1 tags after filtering in treatment: 14440131 INFO @ Wed, 08 Dec 2021 18:20:51: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:20:51: #1 finished! INFO @ Wed, 08 Dec 2021 18:20:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:20:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:20:52: #2 number of paired peaks: 317 WARNING @ Wed, 08 Dec 2021 18:20:52: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Wed, 08 Dec 2021 18:20:52: start model_add_line... INFO @ Wed, 08 Dec 2021 18:20:52: start X-correlation... INFO @ Wed, 08 Dec 2021 18:21:04: end of X-cor INFO @ Wed, 08 Dec 2021 18:21:04: #2 finished! INFO @ Wed, 08 Dec 2021 18:21:04: #2 predicted fragment length is 110 bps INFO @ Wed, 08 Dec 2021 18:21:04: #2 alternative fragment length(s) may be 3,110,143 bps INFO @ Wed, 08 Dec 2021 18:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.20_model.r INFO @ Wed, 08 Dec 2021 18:21:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:21:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:21:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:21:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.10_summits.bed INFO @ Wed, 08 Dec 2021 18:21:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (277 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:21:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:21:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:21:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.05_summits.bed INFO @ Wed, 08 Dec 2021 18:21:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (394 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:21:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:21:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:21:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:21:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342584/SRX10342584.20_summits.bed INFO @ Wed, 08 Dec 2021 18:21:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (175 records, 4 fields): 1 millis CompletedMACS2peakCalling