Job ID = 14159090 SRX = SRX8976736 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13973059 spots for SRR12483280/SRR12483280.sra Written 13973059 spots for SRR12483280/SRR12483280.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159349 ("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: 00:10:59 13973059 reads; of these: 13973059 (100.00%) were paired; of these: 1245097 (8.91%) aligned concordantly 0 times 11056951 (79.13%) aligned concordantly exactly 1 time 1671011 (11.96%) aligned concordantly >1 times ---- 1245097 pairs aligned concordantly 0 times; of these: 912114 (73.26%) aligned discordantly 1 time ---- 332983 pairs aligned 0 times concordantly or discordantly; of these: 665966 mates make up the pairs; of these: 195081 (29.29%) aligned 0 times 216657 (32.53%) aligned exactly 1 time 254228 (38.17%) aligned >1 times 99.30% overall alignment rate Time searching: 00:10:59 Overall time: 00:10:59 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] 411063 / 13613137 = 0.0302 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 19:31:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.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 19:31:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:31:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:31:20: 1000000 INFO @ Wed, 08 Dec 2021 19:31:25: 2000000 INFO @ Wed, 08 Dec 2021 19:31:31: 3000000 INFO @ Wed, 08 Dec 2021 19:31:36: 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 19:31:42: 5000000 INFO @ Wed, 08 Dec 2021 19:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.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 19:31:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:31:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:31:49: 6000000 INFO @ Wed, 08 Dec 2021 19:31:51: 1000000 INFO @ Wed, 08 Dec 2021 19:31:55: 7000000 INFO @ Wed, 08 Dec 2021 19:31:59: 2000000 INFO @ Wed, 08 Dec 2021 19:32:02: 8000000 INFO @ Wed, 08 Dec 2021 19:32:06: 3000000 INFO @ Wed, 08 Dec 2021 19:32:10: 9000000 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 19:32:14: 4000000 INFO @ Wed, 08 Dec 2021 19:32:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.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 19:32:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:32:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:32:18: 10000000 INFO @ Wed, 08 Dec 2021 19:32:20: 5000000 INFO @ Wed, 08 Dec 2021 19:32:24: 1000000 INFO @ Wed, 08 Dec 2021 19:32:26: 11000000 INFO @ Wed, 08 Dec 2021 19:32:27: 6000000 INFO @ Wed, 08 Dec 2021 19:32:31: 2000000 INFO @ Wed, 08 Dec 2021 19:32:33: 12000000 INFO @ Wed, 08 Dec 2021 19:32:35: 7000000 INFO @ Wed, 08 Dec 2021 19:32:39: 3000000 INFO @ Wed, 08 Dec 2021 19:32:41: 13000000 INFO @ Wed, 08 Dec 2021 19:32:43: 8000000 INFO @ Wed, 08 Dec 2021 19:32:46: 4000000 INFO @ Wed, 08 Dec 2021 19:32:48: 14000000 INFO @ Wed, 08 Dec 2021 19:32:50: 9000000 INFO @ Wed, 08 Dec 2021 19:32:51: 5000000 INFO @ Wed, 08 Dec 2021 19:32:57: 15000000 INFO @ Wed, 08 Dec 2021 19:32:57: 10000000 INFO @ Wed, 08 Dec 2021 19:32:58: 6000000 INFO @ Wed, 08 Dec 2021 19:33:03: 11000000 INFO @ Wed, 08 Dec 2021 19:33:04: 16000000 INFO @ Wed, 08 Dec 2021 19:33:06: 7000000 INFO @ Wed, 08 Dec 2021 19:33:11: 12000000 INFO @ Wed, 08 Dec 2021 19:33:12: 17000000 INFO @ Wed, 08 Dec 2021 19:33:14: 8000000 INFO @ Wed, 08 Dec 2021 19:33:19: 18000000 INFO @ Wed, 08 Dec 2021 19:33:19: 13000000 INFO @ Wed, 08 Dec 2021 19:33:22: 9000000 INFO @ Wed, 08 Dec 2021 19:33:26: 19000000 INFO @ Wed, 08 Dec 2021 19:33:27: 14000000 INFO @ Wed, 08 Dec 2021 19:33:29: 10000000 INFO @ Wed, 08 Dec 2021 19:33:34: 20000000 INFO @ Wed, 08 Dec 2021 19:33:35: 15000000 INFO @ Wed, 08 Dec 2021 19:33:35: 11000000 INFO @ Wed, 08 Dec 2021 19:33:41: 12000000 INFO @ Wed, 08 Dec 2021 19:33:41: 21000000 INFO @ Wed, 08 Dec 2021 19:33:42: 16000000 INFO @ Wed, 08 Dec 2021 19:33:49: 13000000 INFO @ Wed, 08 Dec 2021 19:33:49: 22000000 INFO @ Wed, 08 Dec 2021 19:33:51: 17000000 INFO @ Wed, 08 Dec 2021 19:33:57: 18000000 INFO @ Wed, 08 Dec 2021 19:33:57: 23000000 INFO @ Wed, 08 Dec 2021 19:33:58: 14000000 INFO @ Wed, 08 Dec 2021 19:34:05: 15000000 INFO @ Wed, 08 Dec 2021 19:34:05: 19000000 INFO @ Wed, 08 Dec 2021 19:34:05: 24000000 INFO @ Wed, 08 Dec 2021 19:34:11: 20000000 INFO @ Wed, 08 Dec 2021 19:34:12: 25000000 INFO @ Wed, 08 Dec 2021 19:34:12: 16000000 INFO @ Wed, 08 Dec 2021 19:34:18: 21000000 INFO @ Wed, 08 Dec 2021 19:34:18: 26000000 INFO @ Wed, 08 Dec 2021 19:34:19: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:34:25: 22000000 INFO @ Wed, 08 Dec 2021 19:34:25: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:34:25: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:34:25: #1 total tags in treatment: 12337344 INFO @ Wed, 08 Dec 2021 19:34:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:34:25: #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 19:34:25: #1 tags after filtering in treatment: 11520860 INFO @ Wed, 08 Dec 2021 19:34:25: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:34:25: #1 finished! INFO @ Wed, 08 Dec 2021 19:34:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:34:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:34:26: 18000000 INFO @ Wed, 08 Dec 2021 19:34:26: #2 number of paired peaks: 340 WARNING @ Wed, 08 Dec 2021 19:34:26: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Wed, 08 Dec 2021 19:34:26: start model_add_line... INFO @ Wed, 08 Dec 2021 19:34:26: start X-correlation... INFO @ Wed, 08 Dec 2021 19:34:26: end of X-cor INFO @ Wed, 08 Dec 2021 19:34:26: #2 finished! INFO @ Wed, 08 Dec 2021 19:34:26: #2 predicted fragment length is 170 bps INFO @ Wed, 08 Dec 2021 19:34:26: #2 alternative fragment length(s) may be 4,170 bps INFO @ Wed, 08 Dec 2021 19:34:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.05_model.r INFO @ Wed, 08 Dec 2021 19:34:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:34:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:34:30: 23000000 INFO @ Wed, 08 Dec 2021 19:34:33: 19000000 INFO @ Wed, 08 Dec 2021 19:34:38: 24000000 INFO @ Wed, 08 Dec 2021 19:34:39: 20000000 INFO @ Wed, 08 Dec 2021 19:34:45: 25000000 INFO @ Wed, 08 Dec 2021 19:34:45: 21000000 INFO @ Wed, 08 Dec 2021 19:34:51: 22000000 INFO @ Wed, 08 Dec 2021 19:34:52: 26000000 INFO @ Wed, 08 Dec 2021 19:34:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:34:58: 23000000 INFO @ Wed, 08 Dec 2021 19:34:59: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:34:59: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:34:59: #1 total tags in treatment: 12337344 INFO @ Wed, 08 Dec 2021 19:34:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:34:59: #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 19:34:59: #1 tags after filtering in treatment: 11520860 INFO @ Wed, 08 Dec 2021 19:34:59: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:34:59: #1 finished! INFO @ Wed, 08 Dec 2021 19:34:59: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:34:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:35:00: #2 number of paired peaks: 340 WARNING @ Wed, 08 Dec 2021 19:35:00: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Wed, 08 Dec 2021 19:35:00: start model_add_line... INFO @ Wed, 08 Dec 2021 19:35:00: start X-correlation... INFO @ Wed, 08 Dec 2021 19:35:00: end of X-cor INFO @ Wed, 08 Dec 2021 19:35:00: #2 finished! INFO @ Wed, 08 Dec 2021 19:35:00: #2 predicted fragment length is 170 bps INFO @ Wed, 08 Dec 2021 19:35:00: #2 alternative fragment length(s) may be 4,170 bps INFO @ Wed, 08 Dec 2021 19:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.10_model.r INFO @ Wed, 08 Dec 2021 19:35:00: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:35:04: 24000000 INFO @ Wed, 08 Dec 2021 19:35:10: 25000000 INFO @ Wed, 08 Dec 2021 19:35:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:35:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:35:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.05_summits.bed INFO @ Wed, 08 Dec 2021 19:35:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (326 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:35:15: 26000000 INFO @ Wed, 08 Dec 2021 19:35:21: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:35:21: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:35:21: #1 total tags in treatment: 12337344 INFO @ Wed, 08 Dec 2021 19:35:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:35:21: #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 19:35:21: #1 tags after filtering in treatment: 11520860 INFO @ Wed, 08 Dec 2021 19:35:21: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:35:21: #1 finished! INFO @ Wed, 08 Dec 2021 19:35:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:35:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:35:22: #2 number of paired peaks: 340 WARNING @ Wed, 08 Dec 2021 19:35:22: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Wed, 08 Dec 2021 19:35:22: start model_add_line... INFO @ Wed, 08 Dec 2021 19:35:22: start X-correlation... INFO @ Wed, 08 Dec 2021 19:35:23: end of X-cor INFO @ Wed, 08 Dec 2021 19:35:23: #2 finished! INFO @ Wed, 08 Dec 2021 19:35:23: #2 predicted fragment length is 170 bps INFO @ Wed, 08 Dec 2021 19:35:23: #2 alternative fragment length(s) may be 4,170 bps INFO @ Wed, 08 Dec 2021 19:35:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.20_model.r INFO @ Wed, 08 Dec 2021 19:35:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:35:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:35:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:35:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:35:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:35:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.10_summits.bed INFO @ Wed, 08 Dec 2021 19:35:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:35:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:36:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:36:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:36:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976736/SRX8976736.20_summits.bed INFO @ Wed, 08 Dec 2021 19:36:02: Done! pass1 - making usageList (7 chroms): 30 millis pass2 - checking and writing primary data (169 records, 4 fields): 36 millis CompletedMACS2peakCalling