Job ID = 5791132 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:37:30 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 8,809,763 reads read : 17,619,526 reads written : 17,619,526 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: 00:07:33 8809763 reads; of these: 8809763 (100.00%) were paired; of these: 1724555 (19.58%) aligned concordantly 0 times 5121340 (58.13%) aligned concordantly exactly 1 time 1963868 (22.29%) aligned concordantly >1 times ---- 1724555 pairs aligned concordantly 0 times; of these: 522260 (30.28%) aligned discordantly 1 time ---- 1202295 pairs aligned 0 times concordantly or discordantly; of these: 2404590 mates make up the pairs; of these: 1983638 (82.49%) aligned 0 times 99510 (4.14%) aligned exactly 1 time 321442 (13.37%) aligned >1 times 88.74% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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] 1998890 / 7556381 = 0.2645 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 08:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.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 08:56:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:56:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:56:26: 1000000 INFO @ Wed, 22 Apr 2020 08:56:31: 2000000 INFO @ Wed, 22 Apr 2020 08:56:36: 3000000 INFO @ Wed, 22 Apr 2020 08:56:42: 4000000 INFO @ Wed, 22 Apr 2020 08:56:47: 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 08:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.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 08:56:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:56:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:56:52: 6000000 INFO @ Wed, 22 Apr 2020 08:56:57: 1000000 INFO @ Wed, 22 Apr 2020 08:56:57: 7000000 INFO @ Wed, 22 Apr 2020 08:57:03: 8000000 INFO @ Wed, 22 Apr 2020 08:57:04: 2000000 INFO @ Wed, 22 Apr 2020 08:57:08: 9000000 INFO @ Wed, 22 Apr 2020 08:57:10: 3000000 INFO @ Wed, 22 Apr 2020 08:57:14: 10000000 INFO @ Wed, 22 Apr 2020 08:57:17: 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 08:57:19: 11000000 INFO @ Wed, 22 Apr 2020 08:57:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.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 08:57:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:57:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:57:23: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 08:57:23: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 08:57:23: #1 total tags in treatment: 5147503 INFO @ Wed, 22 Apr 2020 08:57:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:57:23: #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 08:57:23: #1 tags after filtering in treatment: 3243789 INFO @ Wed, 22 Apr 2020 08:57:23: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 22 Apr 2020 08:57:23: #1 finished! INFO @ Wed, 22 Apr 2020 08:57:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:57:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:57:23: #2 number of paired peaks: 25 WARNING @ Wed, 22 Apr 2020 08:57:23: Too few paired peaks (25) 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 08:57:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.05_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/SRX6614926/SRX6614926.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:57:24: 5000000 INFO @ Wed, 22 Apr 2020 08:57:26: 1000000 INFO @ Wed, 22 Apr 2020 08:57:30: 6000000 INFO @ Wed, 22 Apr 2020 08:57:31: 2000000 INFO @ Wed, 22 Apr 2020 08:57:37: 3000000 INFO @ Wed, 22 Apr 2020 08:57:37: 7000000 INFO @ Wed, 22 Apr 2020 08:57:43: 4000000 INFO @ Wed, 22 Apr 2020 08:57:44: 8000000 INFO @ Wed, 22 Apr 2020 08:57:48: 5000000 INFO @ Wed, 22 Apr 2020 08:57:50: 9000000 INFO @ Wed, 22 Apr 2020 08:57:54: 6000000 INFO @ Wed, 22 Apr 2020 08:57:56: 10000000 INFO @ Wed, 22 Apr 2020 08:57:59: 7000000 INFO @ Wed, 22 Apr 2020 08:58:02: 11000000 INFO @ Wed, 22 Apr 2020 08:58:05: 8000000 INFO @ Wed, 22 Apr 2020 08:58:07: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 08:58:07: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 08:58:07: #1 total tags in treatment: 5147503 INFO @ Wed, 22 Apr 2020 08:58:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:58:07: #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 08:58:07: #1 tags after filtering in treatment: 3243789 INFO @ Wed, 22 Apr 2020 08:58:07: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 22 Apr 2020 08:58:07: #1 finished! INFO @ Wed, 22 Apr 2020 08:58:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:58:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:58:07: #2 number of paired peaks: 25 WARNING @ Wed, 22 Apr 2020 08:58:07: Too few paired peaks (25) 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 08:58:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.10_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/SRX6614926/SRX6614926.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:58:10: 9000000 INFO @ Wed, 22 Apr 2020 08:58:16: 10000000 INFO @ Wed, 22 Apr 2020 08:58:21: 11000000 INFO @ Wed, 22 Apr 2020 08:58:25: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 08:58:25: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 08:58:25: #1 total tags in treatment: 5147503 INFO @ Wed, 22 Apr 2020 08:58:25: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:58:25: #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 08:58:25: #1 tags after filtering in treatment: 3243789 INFO @ Wed, 22 Apr 2020 08:58:25: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 22 Apr 2020 08:58:25: #1 finished! INFO @ Wed, 22 Apr 2020 08:58:25: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:58:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:58:25: #2 number of paired peaks: 25 WARNING @ Wed, 22 Apr 2020 08:58:25: Too few paired peaks (25) 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 08:58:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.20_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/SRX6614926/SRX6614926.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614926/SRX6614926.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。