Job ID = 5791800 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,480,949 reads read : 18,961,898 reads written : 18,961,898 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: 00:06:07 9480949 reads; of these: 9480949 (100.00%) were paired; of these: 2207246 (23.28%) aligned concordantly 0 times 6331794 (66.78%) aligned concordantly exactly 1 time 941909 (9.93%) aligned concordantly >1 times ---- 2207246 pairs aligned concordantly 0 times; of these: 737903 (33.43%) aligned discordantly 1 time ---- 1469343 pairs aligned 0 times concordantly or discordantly; of these: 2938686 mates make up the pairs; of these: 2533790 (86.22%) aligned 0 times 167150 (5.69%) aligned exactly 1 time 237746 (8.09%) aligned >1 times 86.64% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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 8 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] 2207739 / 7958352 = 0.2774 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 11:01:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.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 11:01:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:01:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:02:00: 1000000 INFO @ Wed, 22 Apr 2020 11:02:07: 2000000 INFO @ Wed, 22 Apr 2020 11:02:14: 3000000 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 11:02:21: 4000000 INFO @ Wed, 22 Apr 2020 11:02:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.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 11:02:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:02:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:02:29: 5000000 INFO @ Wed, 22 Apr 2020 11:02:30: 1000000 INFO @ Wed, 22 Apr 2020 11:02:36: 6000000 INFO @ Wed, 22 Apr 2020 11:02:37: 2000000 INFO @ Wed, 22 Apr 2020 11:02:44: 7000000 INFO @ Wed, 22 Apr 2020 11:02:45: 3000000 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 11:02:52: 8000000 INFO @ Wed, 22 Apr 2020 11:02:52: 4000000 INFO @ Wed, 22 Apr 2020 11:02:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.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 11:02:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:02:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:02:59: 9000000 INFO @ Wed, 22 Apr 2020 11:03:00: 5000000 INFO @ Wed, 22 Apr 2020 11:03:00: 1000000 INFO @ Wed, 22 Apr 2020 11:03:07: 10000000 INFO @ Wed, 22 Apr 2020 11:03:07: 6000000 INFO @ Wed, 22 Apr 2020 11:03:08: 2000000 INFO @ Wed, 22 Apr 2020 11:03:15: 11000000 INFO @ Wed, 22 Apr 2020 11:03:15: 7000000 INFO @ Wed, 22 Apr 2020 11:03:16: 3000000 INFO @ Wed, 22 Apr 2020 11:03:22: 8000000 INFO @ Wed, 22 Apr 2020 11:03:22: 12000000 INFO @ Wed, 22 Apr 2020 11:03:23: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:03:23: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:03:23: #1 total tags in treatment: 5243494 INFO @ Wed, 22 Apr 2020 11:03:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:03:23: #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 11:03:23: #1 tags after filtering in treatment: 2747403 INFO @ Wed, 22 Apr 2020 11:03:23: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Apr 2020 11:03:23: #1 finished! INFO @ Wed, 22 Apr 2020 11:03:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:03:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:03:23: #2 number of paired peaks: 1 WARNING @ Wed, 22 Apr 2020 11:03:23: Too few paired peaks (1) 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 11:03:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.05_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/SRX7756595/SRX7756595.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:03:23: 4000000 INFO @ Wed, 22 Apr 2020 11:03:30: 9000000 INFO @ Wed, 22 Apr 2020 11:03:31: 5000000 INFO @ Wed, 22 Apr 2020 11:03:37: 10000000 INFO @ Wed, 22 Apr 2020 11:03:38: 6000000 INFO @ Wed, 22 Apr 2020 11:03:45: 11000000 INFO @ Wed, 22 Apr 2020 11:03:46: 7000000 INFO @ Wed, 22 Apr 2020 11:03:52: 12000000 INFO @ Wed, 22 Apr 2020 11:03:52: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:03:52: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:03:52: #1 total tags in treatment: 5243494 INFO @ Wed, 22 Apr 2020 11:03:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:03:52: #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 11:03:52: #1 tags after filtering in treatment: 2747403 INFO @ Wed, 22 Apr 2020 11:03:52: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Apr 2020 11:03:52: #1 finished! INFO @ Wed, 22 Apr 2020 11:03:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:03:52: #2 number of paired peaks: 1 WARNING @ Wed, 22 Apr 2020 11:03:52: Too few paired peaks (1) 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 11:03:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.10_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/SRX7756595/SRX7756595.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:03:53: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:04:00: 9000000 INFO @ Wed, 22 Apr 2020 11:04:07: 10000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:04:14: 11000000 INFO @ Wed, 22 Apr 2020 11:04:20: 12000000 INFO @ Wed, 22 Apr 2020 11:04:21: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:04:21: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:04:21: #1 total tags in treatment: 5243494 INFO @ Wed, 22 Apr 2020 11:04:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:04:21: #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 11:04:21: #1 tags after filtering in treatment: 2747403 INFO @ Wed, 22 Apr 2020 11:04:21: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Apr 2020 11:04:21: #1 finished! INFO @ Wed, 22 Apr 2020 11:04:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:04:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:04:21: #2 number of paired peaks: 1 WARNING @ Wed, 22 Apr 2020 11:04:21: Too few paired peaks (1) 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 11:04:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.20_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/SRX7756595/SRX7756595.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756595/SRX7756595.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling