Job ID = 5791207 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 14,263,949 reads read : 28,527,898 reads written : 28,527,898 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: 00:11:35 14263949 reads; of these: 14263949 (100.00%) were paired; of these: 3470022 (24.33%) aligned concordantly 0 times 5754280 (40.34%) aligned concordantly exactly 1 time 5039647 (35.33%) aligned concordantly >1 times ---- 3470022 pairs aligned concordantly 0 times; of these: 528306 (15.22%) aligned discordantly 1 time ---- 2941716 pairs aligned 0 times concordantly or discordantly; of these: 5883432 mates make up the pairs; of these: 4840528 (82.27%) aligned 0 times 186215 (3.17%) aligned exactly 1 time 856689 (14.56%) aligned >1 times 83.03% overall alignment rate Time searching: 00:11:35 Overall time: 00:11:35 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 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 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] 5316375 / 11245424 = 0.4728 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 09:31:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.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 09:31:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:31:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:31:19: 1000000 INFO @ Wed, 22 Apr 2020 09:31:24: 2000000 INFO @ Wed, 22 Apr 2020 09:31:30: 3000000 INFO @ Wed, 22 Apr 2020 09:31:35: 4000000 INFO @ Wed, 22 Apr 2020 09:31:40: 5000000 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 09:31:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.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 09:31:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:31:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:31:46: 6000000 INFO @ Wed, 22 Apr 2020 09:31:50: 1000000 INFO @ Wed, 22 Apr 2020 09:31:51: 7000000 INFO @ Wed, 22 Apr 2020 09:31:56: 2000000 INFO @ Wed, 22 Apr 2020 09:31:56: 8000000 INFO @ Wed, 22 Apr 2020 09:32:01: 9000000 INFO @ Wed, 22 Apr 2020 09:32:02: 3000000 INFO @ Wed, 22 Apr 2020 09:32:06: 10000000 INFO @ Wed, 22 Apr 2020 09:32:08: 4000000 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 09:32:12: 11000000 INFO @ Wed, 22 Apr 2020 09:32:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.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 09:32:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:32:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:32:15: 5000000 INFO @ Wed, 22 Apr 2020 09:32:17: 12000000 INFO @ Wed, 22 Apr 2020 09:32:21: 1000000 INFO @ Wed, 22 Apr 2020 09:32:21: 6000000 INFO @ Wed, 22 Apr 2020 09:32:22: 13000000 INFO @ Wed, 22 Apr 2020 09:32:23: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:32:23: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:32:23: #1 total tags in treatment: 5574495 INFO @ Wed, 22 Apr 2020 09:32:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:32:23: #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 09:32:23: #1 tags after filtering in treatment: 3326483 INFO @ Wed, 22 Apr 2020 09:32:23: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 09:32:23: #1 finished! INFO @ Wed, 22 Apr 2020 09:32:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:32:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:32:23: #2 number of paired peaks: 27 WARNING @ Wed, 22 Apr 2020 09:32:23: Too few paired peaks (27) 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 09:32:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.05_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/SRX6614996/SRX6614996.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:32:27: 7000000 INFO @ Wed, 22 Apr 2020 09:32:28: 2000000 INFO @ Wed, 22 Apr 2020 09:32:34: 8000000 INFO @ Wed, 22 Apr 2020 09:32:35: 3000000 INFO @ Wed, 22 Apr 2020 09:32:40: 9000000 INFO @ Wed, 22 Apr 2020 09:32:41: 4000000 INFO @ Wed, 22 Apr 2020 09:32:46: 10000000 INFO @ Wed, 22 Apr 2020 09:32:48: 5000000 INFO @ Wed, 22 Apr 2020 09:32:52: 11000000 INFO @ Wed, 22 Apr 2020 09:32:55: 6000000 INFO @ Wed, 22 Apr 2020 09:32:58: 12000000 INFO @ Wed, 22 Apr 2020 09:33:02: 7000000 INFO @ Wed, 22 Apr 2020 09:33:04: 13000000 INFO @ Wed, 22 Apr 2020 09:33:04: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:33:04: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:33:04: #1 total tags in treatment: 5574495 INFO @ Wed, 22 Apr 2020 09:33:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:33:04: #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 09:33:04: #1 tags after filtering in treatment: 3326483 INFO @ Wed, 22 Apr 2020 09:33:04: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 09:33:04: #1 finished! INFO @ Wed, 22 Apr 2020 09:33:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:33:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:33:04: #2 number of paired peaks: 27 WARNING @ Wed, 22 Apr 2020 09:33:04: Too few paired peaks (27) 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 09:33:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.10_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/SRX6614996/SRX6614996.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:33:08: 8000000 INFO @ Wed, 22 Apr 2020 09:33:14: 9000000 INFO @ Wed, 22 Apr 2020 09:33:21: 10000000 INFO @ Wed, 22 Apr 2020 09:33:27: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:33:34: 12000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:33:40: 13000000 INFO @ Wed, 22 Apr 2020 09:33:40: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:33:40: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:33:40: #1 total tags in treatment: 5574495 INFO @ Wed, 22 Apr 2020 09:33:40: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:33:40: #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 09:33:40: #1 tags after filtering in treatment: 3326483 INFO @ Wed, 22 Apr 2020 09:33:40: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 09:33:40: #1 finished! INFO @ Wed, 22 Apr 2020 09:33:40: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:33:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:33:41: #2 number of paired peaks: 27 WARNING @ Wed, 22 Apr 2020 09:33:41: Too few paired peaks (27) 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 09:33:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.20_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/SRX6614996/SRX6614996.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614996/SRX6614996.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling