Job ID = 5791151 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:39:10 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 ) 2020-04-21T23:55:49 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 : 14,311,329 reads read : 28,622,658 reads written : 28,622,658 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: 00:17:55 14311329 reads; of these: 14311329 (100.00%) were paired; of these: 7787732 (54.42%) aligned concordantly 0 times 3327496 (23.25%) aligned concordantly exactly 1 time 3196101 (22.33%) aligned concordantly >1 times ---- 7787732 pairs aligned concordantly 0 times; of these: 2446563 (31.42%) aligned discordantly 1 time ---- 5341169 pairs aligned 0 times concordantly or discordantly; of these: 10682338 mates make up the pairs; of these: 7083213 (66.31%) aligned 0 times 442305 (4.14%) aligned exactly 1 time 3156820 (29.55%) aligned >1 times 75.25% overall alignment rate Time searching: 00:17:55 Overall time: 00:17:55 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 16 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] 3898004 / 8797482 = 0.4431 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 09:30:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.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 09:30:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:30:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:30:20: 1000000 INFO @ Wed, 22 Apr 2020 09:30:27: 2000000 INFO @ Wed, 22 Apr 2020 09:30:34: 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 09:30:42: 4000000 INFO @ Wed, 22 Apr 2020 09:30:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.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 09:30:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:30:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:30:49: 5000000 INFO @ Wed, 22 Apr 2020 09:30:51: 1000000 INFO @ Wed, 22 Apr 2020 09:30:57: 6000000 INFO @ Wed, 22 Apr 2020 09:30:59: 2000000 INFO @ Wed, 22 Apr 2020 09:31:05: 7000000 INFO @ Wed, 22 Apr 2020 09:31:07: 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 09:31:13: 8000000 INFO @ Wed, 22 Apr 2020 09:31:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.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 09:31:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:31:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:31:15: 4000000 INFO @ Wed, 22 Apr 2020 09:31:21: 9000000 INFO @ Wed, 22 Apr 2020 09:31:21: 1000000 INFO @ Wed, 22 Apr 2020 09:31:23: 5000000 INFO @ Wed, 22 Apr 2020 09:31:29: 10000000 INFO @ Wed, 22 Apr 2020 09:31:30: 2000000 INFO @ Wed, 22 Apr 2020 09:31:32: 6000000 INFO @ Wed, 22 Apr 2020 09:31:36: 11000000 INFO @ Wed, 22 Apr 2020 09:31:38: 3000000 INFO @ Wed, 22 Apr 2020 09:31:40: 7000000 INFO @ Wed, 22 Apr 2020 09:31:44: 12000000 INFO @ Wed, 22 Apr 2020 09:31:46: 4000000 INFO @ Wed, 22 Apr 2020 09:31:47: 8000000 INFO @ Wed, 22 Apr 2020 09:31:52: 13000000 INFO @ Wed, 22 Apr 2020 09:31:54: 5000000 INFO @ Wed, 22 Apr 2020 09:31:55: 9000000 INFO @ Wed, 22 Apr 2020 09:31:58: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:31:58: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:31:58: #1 total tags in treatment: 3240226 INFO @ Wed, 22 Apr 2020 09:31:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:31:58: #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 09:31:58: #1 tags after filtering in treatment: 2085357 INFO @ Wed, 22 Apr 2020 09:31:58: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 09:31:58: #1 finished! INFO @ Wed, 22 Apr 2020 09:31:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:31:58: #2 number of paired peaks: 27 WARNING @ Wed, 22 Apr 2020 09:31:58: 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 09:31:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.05_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/SRX6614944/SRX6614944.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:32:02: 6000000 INFO @ Wed, 22 Apr 2020 09:32:03: 10000000 INFO @ Wed, 22 Apr 2020 09:32:10: 7000000 INFO @ Wed, 22 Apr 2020 09:32:11: 11000000 INFO @ Wed, 22 Apr 2020 09:32:17: 8000000 INFO @ Wed, 22 Apr 2020 09:32:18: 12000000 INFO @ Wed, 22 Apr 2020 09:32:25: 9000000 INFO @ Wed, 22 Apr 2020 09:32:26: 13000000 INFO @ Wed, 22 Apr 2020 09:32:32: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:32:32: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:32:32: #1 total tags in treatment: 3240226 INFO @ Wed, 22 Apr 2020 09:32:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:32:32: #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 09:32:32: #1 tags after filtering in treatment: 2085357 INFO @ Wed, 22 Apr 2020 09:32:32: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 09:32:32: #1 finished! INFO @ Wed, 22 Apr 2020 09:32:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:32:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:32:32: #2 number of paired peaks: 27 WARNING @ Wed, 22 Apr 2020 09:32:32: 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 09:32:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.10_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/SRX6614944/SRX6614944.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:32:33: 10000000 INFO @ Wed, 22 Apr 2020 09:32:40: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:32:48: 12000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:32:55: 13000000 INFO @ Wed, 22 Apr 2020 09:33:01: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:33:01: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:33:01: #1 total tags in treatment: 3240226 INFO @ Wed, 22 Apr 2020 09:33:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:33:01: #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 09:33:01: #1 tags after filtering in treatment: 2085357 INFO @ Wed, 22 Apr 2020 09:33:01: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 09:33:01: #1 finished! INFO @ Wed, 22 Apr 2020 09:33:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:33:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:33:01: #2 number of paired peaks: 27 WARNING @ Wed, 22 Apr 2020 09:33:01: 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 09:33:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.20_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/SRX6614944/SRX6614944.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614944/SRX6614944.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling