Job ID = 5791621 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 1900-01-00T00:00:00 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 ) 2020-04-22T00:39:38 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 ) 2020-04-22T00:41:11 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 ) 2020-04-22T00:43:56 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 ) 2020-04-22T00:43:56 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 ) 2020-04-22T00:45:24 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 ) 2020-04-22T00:52:23 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 ) 2020-04-22T00:52:23 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 : 33,682,151 reads read : 67,364,302 reads written : 67,364,302 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: 00:09:53 33682151 reads; of these: 33682151 (100.00%) were paired; of these: 16245973 (48.23%) aligned concordantly 0 times 15755203 (46.78%) aligned concordantly exactly 1 time 1680975 (4.99%) aligned concordantly >1 times ---- 16245973 pairs aligned concordantly 0 times; of these: 31740 (0.20%) aligned discordantly 1 time ---- 16214233 pairs aligned 0 times concordantly or discordantly; of these: 32428466 mates make up the pairs; of these: 31972792 (98.59%) aligned 0 times 399816 (1.23%) aligned exactly 1 time 55858 (0.17%) aligned >1 times 52.54% overall alignment rate Time searching: 00:09:53 Overall time: 00:09:53 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] 10799203 / 17446074 = 0.6190 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 10:15:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.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 10:15:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:15:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:15:40: 1000000 INFO @ Wed, 22 Apr 2020 10:15:44: 2000000 INFO @ Wed, 22 Apr 2020 10:15:49: 3000000 INFO @ Wed, 22 Apr 2020 10:15:54: 4000000 INFO @ Wed, 22 Apr 2020 10:15:58: 5000000 INFO @ Wed, 22 Apr 2020 10:16:03: 6000000 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 10:16:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.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 10:16:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:16:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:16:08: 7000000 INFO @ Wed, 22 Apr 2020 10:16:10: 1000000 INFO @ Wed, 22 Apr 2020 10:16:13: 8000000 INFO @ Wed, 22 Apr 2020 10:16:15: 2000000 INFO @ Wed, 22 Apr 2020 10:16:18: 9000000 INFO @ Wed, 22 Apr 2020 10:16:20: 3000000 INFO @ Wed, 22 Apr 2020 10:16:24: 10000000 INFO @ Wed, 22 Apr 2020 10:16:26: 4000000 INFO @ Wed, 22 Apr 2020 10:16:29: 11000000 INFO @ Wed, 22 Apr 2020 10:16:31: 5000000 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 10:16:34: 12000000 INFO @ Wed, 22 Apr 2020 10:16:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.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 10:16:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:16:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:16:36: 6000000 INFO @ Wed, 22 Apr 2020 10:16:39: 13000000 INFO @ Wed, 22 Apr 2020 10:16:40: 1000000 INFO @ Wed, 22 Apr 2020 10:16:41: 7000000 INFO @ Wed, 22 Apr 2020 10:16:43: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:16:43: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:16:43: #1 total tags in treatment: 6640641 INFO @ Wed, 22 Apr 2020 10:16:43: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:16:43: #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 10:16:43: #1 tags after filtering in treatment: 5504131 INFO @ Wed, 22 Apr 2020 10:16:43: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 10:16:43: #1 finished! INFO @ Wed, 22 Apr 2020 10:16:43: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:16:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:16:44: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:16:44: 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 10:16:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.05_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/SRX7409589/SRX7409589.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:16:45: 2000000 INFO @ Wed, 22 Apr 2020 10:16:47: 8000000 INFO @ Wed, 22 Apr 2020 10:16:51: 3000000 INFO @ Wed, 22 Apr 2020 10:16:52: 9000000 INFO @ Wed, 22 Apr 2020 10:16:56: 4000000 INFO @ Wed, 22 Apr 2020 10:16:57: 10000000 INFO @ Wed, 22 Apr 2020 10:17:01: 5000000 INFO @ Wed, 22 Apr 2020 10:17:02: 11000000 INFO @ Wed, 22 Apr 2020 10:17:07: 6000000 INFO @ Wed, 22 Apr 2020 10:17:07: 12000000 INFO @ Wed, 22 Apr 2020 10:17:12: 7000000 INFO @ Wed, 22 Apr 2020 10:17:13: 13000000 INFO @ Wed, 22 Apr 2020 10:17:17: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:17:17: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:17:17: #1 total tags in treatment: 6640641 INFO @ Wed, 22 Apr 2020 10:17:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:17:17: #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 10:17:17: #1 tags after filtering in treatment: 5504131 INFO @ Wed, 22 Apr 2020 10:17:17: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 10:17:17: #1 finished! INFO @ Wed, 22 Apr 2020 10:17:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:17:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:17:17: 8000000 INFO @ Wed, 22 Apr 2020 10:17:17: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:17:17: 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 10:17:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.10_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/SRX7409589/SRX7409589.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:17:22: 9000000 INFO @ Wed, 22 Apr 2020 10:17:27: 10000000 INFO @ Wed, 22 Apr 2020 10:17:32: 11000000 INFO @ Wed, 22 Apr 2020 10:17:37: 12000000 INFO @ Wed, 22 Apr 2020 10:17:42: 13000000 INFO @ Wed, 22 Apr 2020 10:17:45: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:17:45: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:17:45: #1 total tags in treatment: 6640641 INFO @ Wed, 22 Apr 2020 10:17:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:17:45: #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 10:17:46: #1 tags after filtering in treatment: 5504131 INFO @ Wed, 22 Apr 2020 10:17:46: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 10:17:46: #1 finished! INFO @ Wed, 22 Apr 2020 10:17:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:17:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:17:46: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:17:46: 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 10:17:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.20_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/SRX7409589/SRX7409589.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409589/SRX7409589.20_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。