Job ID = 5791680 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 20,420,749 reads read : 40,841,498 reads written : 40,841,498 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:21:36 20420749 reads; of these: 20420749 (100.00%) were paired; of these: 6981345 (34.19%) aligned concordantly 0 times 11163141 (54.67%) aligned concordantly exactly 1 time 2276263 (11.15%) aligned concordantly >1 times ---- 6981345 pairs aligned concordantly 0 times; of these: 1523527 (21.82%) aligned discordantly 1 time ---- 5457818 pairs aligned 0 times concordantly or discordantly; of these: 10915636 mates make up the pairs; of these: 9532456 (87.33%) aligned 0 times 615741 (5.64%) aligned exactly 1 time 767439 (7.03%) aligned >1 times 76.66% overall alignment rate Time searching: 00:21:36 Overall time: 00:21:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 24 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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 4530667 / 14867770 = 0.3047 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 11:36:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.bam'] # control file = None # effective genome size = 1.21e+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, 22 Apr 2020 11:36:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:36:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:36:10: 1000000 INFO @ Wed, 22 Apr 2020 11:36:19: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 11:36:29: 3000000 INFO @ Wed, 22 Apr 2020 11:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.bam'] # control file = None # effective genome size = 1.21e+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, 22 Apr 2020 11:36:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:36:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:36:39: 4000000 INFO @ Wed, 22 Apr 2020 11:36:40: 1000000 INFO @ Wed, 22 Apr 2020 11:36:49: 5000000 INFO @ Wed, 22 Apr 2020 11:36:49: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 11:36:58: 3000000 INFO @ Wed, 22 Apr 2020 11:36:59: 6000000 INFO @ Wed, 22 Apr 2020 11:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.bam'] # control file = None # effective genome size = 1.21e+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, 22 Apr 2020 11:37:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:37:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:37:07: 4000000 INFO @ Wed, 22 Apr 2020 11:37:09: 7000000 INFO @ Wed, 22 Apr 2020 11:37:11: 1000000 INFO @ Wed, 22 Apr 2020 11:37:17: 5000000 INFO @ Wed, 22 Apr 2020 11:37:20: 8000000 INFO @ Wed, 22 Apr 2020 11:37:21: 2000000 INFO @ Wed, 22 Apr 2020 11:37:27: 6000000 INFO @ Wed, 22 Apr 2020 11:37:30: 3000000 INFO @ Wed, 22 Apr 2020 11:37:31: 9000000 INFO @ Wed, 22 Apr 2020 11:37:36: 7000000 INFO @ Wed, 22 Apr 2020 11:37:40: 4000000 INFO @ Wed, 22 Apr 2020 11:37:41: 10000000 INFO @ Wed, 22 Apr 2020 11:37:46: 8000000 INFO @ Wed, 22 Apr 2020 11:37:49: 5000000 INFO @ Wed, 22 Apr 2020 11:37:52: 11000000 INFO @ Wed, 22 Apr 2020 11:37:55: 9000000 INFO @ Wed, 22 Apr 2020 11:37:59: 6000000 INFO @ Wed, 22 Apr 2020 11:38:02: 12000000 INFO @ Wed, 22 Apr 2020 11:38:05: 10000000 INFO @ Wed, 22 Apr 2020 11:38:09: 7000000 INFO @ Wed, 22 Apr 2020 11:38:12: 13000000 INFO @ Wed, 22 Apr 2020 11:38:14: 11000000 INFO @ Wed, 22 Apr 2020 11:38:18: 8000000 INFO @ Wed, 22 Apr 2020 11:38:23: 14000000 INFO @ Wed, 22 Apr 2020 11:38:24: 12000000 INFO @ Wed, 22 Apr 2020 11:38:28: 9000000 INFO @ Wed, 22 Apr 2020 11:38:33: 15000000 INFO @ Wed, 22 Apr 2020 11:38:33: 13000000 INFO @ Wed, 22 Apr 2020 11:38:37: 10000000 INFO @ Wed, 22 Apr 2020 11:38:43: 16000000 INFO @ Wed, 22 Apr 2020 11:38:43: 14000000 INFO @ Wed, 22 Apr 2020 11:38:47: 11000000 INFO @ Wed, 22 Apr 2020 11:38:52: 15000000 INFO @ Wed, 22 Apr 2020 11:38:53: 17000000 INFO @ Wed, 22 Apr 2020 11:38:56: 12000000 INFO @ Wed, 22 Apr 2020 11:39:01: 16000000 INFO @ Wed, 22 Apr 2020 11:39:03: 18000000 INFO @ Wed, 22 Apr 2020 11:39:05: 13000000 INFO @ Wed, 22 Apr 2020 11:39:11: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:39:13: 19000000 INFO @ Wed, 22 Apr 2020 11:39:15: 14000000 INFO @ Wed, 22 Apr 2020 11:39:20: 18000000 INFO @ Wed, 22 Apr 2020 11:39:24: 20000000 INFO @ Wed, 22 Apr 2020 11:39:24: 15000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:39:29: 19000000 INFO @ Wed, 22 Apr 2020 11:39:33: 16000000 INFO @ Wed, 22 Apr 2020 11:39:34: 21000000 INFO @ Wed, 22 Apr 2020 11:39:39: 20000000 INFO @ Wed, 22 Apr 2020 11:39:42: 17000000 INFO @ Wed, 22 Apr 2020 11:39:44: 22000000 INFO @ Wed, 22 Apr 2020 11:39:46: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:39:46: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:39:46: #1 total tags in treatment: 9178103 INFO @ Wed, 22 Apr 2020 11:39:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:39:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 11:39:46: #1 tags after filtering in treatment: 6513613 INFO @ Wed, 22 Apr 2020 11:39:46: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 22 Apr 2020 11:39:46: #1 finished! INFO @ Wed, 22 Apr 2020 11:39:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:39:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:39:47: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:39:47: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 11:39:47: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 11:39:48: 21000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:39:52: 18000000 INFO @ Wed, 22 Apr 2020 11:39:57: 22000000 INFO @ Wed, 22 Apr 2020 11:39:59: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:39:59: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:39:59: #1 total tags in treatment: 9178103 INFO @ Wed, 22 Apr 2020 11:39:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:39:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 11:39:59: #1 tags after filtering in treatment: 6513613 INFO @ Wed, 22 Apr 2020 11:39:59: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 22 Apr 2020 11:39:59: #1 finished! INFO @ Wed, 22 Apr 2020 11:39:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:39:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:40:00: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:40:00: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 11:40:00: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 11:40:00: 19000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:40:08: 20000000 INFO @ Wed, 22 Apr 2020 11:40:16: 21000000 INFO @ Wed, 22 Apr 2020 11:40:24: 22000000 INFO @ Wed, 22 Apr 2020 11:40:26: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:40:26: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:40:26: #1 total tags in treatment: 9178103 INFO @ Wed, 22 Apr 2020 11:40:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:40:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 11:40:26: #1 tags after filtering in treatment: 6513613 INFO @ Wed, 22 Apr 2020 11:40:26: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 22 Apr 2020 11:40:26: #1 finished! INFO @ Wed, 22 Apr 2020 11:40:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:40:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:40:27: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:40:27: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 11:40:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409639/SRX7409639.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling