Job ID = 5791630 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:49:47 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 ) 2020-04-22T00:50:13 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 ) 2020-04-22T00:50:13 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 ) 2020-04-22T00:50:13 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 ) 2020-04-22T00:52:56 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 ) 2020-04-22T00:54:43 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 ) 2020-04-22T01:23:28 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 ) 2020-04-22T01:38:45 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 : 91,984,091 reads read : 183,968,182 reads written : 183,968,182 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: 00:09:16 91984091 reads; of these: 91984091 (100.00%) were paired; of these: 82587020 (89.78%) aligned concordantly 0 times 8411099 (9.14%) aligned concordantly exactly 1 time 985972 (1.07%) aligned concordantly >1 times ---- 82587020 pairs aligned concordantly 0 times; of these: 17393 (0.02%) aligned discordantly 1 time ---- 82569627 pairs aligned 0 times concordantly or discordantly; of these: 165139254 mates make up the pairs; of these: 164873162 (99.84%) aligned 0 times 231080 (0.14%) aligned exactly 1 time 35012 (0.02%) aligned >1 times 10.38% overall alignment rate Time searching: 00:09:16 Overall time: 00:09:16 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] 4311325 / 9406966 = 0.4583 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 10:57:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.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 10:57:09: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:57:09: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:57:15: 1000000 INFO @ Wed, 22 Apr 2020 10:57:21: 2000000 INFO @ Wed, 22 Apr 2020 10:57:26: 3000000 INFO @ Wed, 22 Apr 2020 10:57:32: 4000000 INFO @ Wed, 22 Apr 2020 10:57:37: 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 10:57:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.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 10:57:39: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:57:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:57:43: 6000000 INFO @ Wed, 22 Apr 2020 10:57:47: 1000000 INFO @ Wed, 22 Apr 2020 10:57:50: 7000000 INFO @ Wed, 22 Apr 2020 10:57:54: 2000000 INFO @ Wed, 22 Apr 2020 10:57:56: 8000000 INFO @ Wed, 22 Apr 2020 10:58:02: 3000000 INFO @ Wed, 22 Apr 2020 10:58:02: 9000000 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 10:58:09: 10000000 INFO @ Wed, 22 Apr 2020 10:58:09: 4000000 INFO @ Wed, 22 Apr 2020 10:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.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 10:58:09: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:58:09: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:58:12: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:58:12: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:58:12: #1 total tags in treatment: 5093318 INFO @ Wed, 22 Apr 2020 10:58:12: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:58:12: #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 10:58:12: #1 tags after filtering in treatment: 4148492 INFO @ Wed, 22 Apr 2020 10:58:12: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 10:58:12: #1 finished! INFO @ Wed, 22 Apr 2020 10:58:12: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:58:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:58:12: #2 number of paired peaks: 44 WARNING @ Wed, 22 Apr 2020 10:58:12: Too few paired peaks (44) 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 10:58:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.05_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/SRX7409598/SRX7409598.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:58:16: 1000000 INFO @ Wed, 22 Apr 2020 10:58:17: 5000000 INFO @ Wed, 22 Apr 2020 10:58:23: 2000000 INFO @ Wed, 22 Apr 2020 10:58:24: 6000000 INFO @ Wed, 22 Apr 2020 10:58:29: 3000000 INFO @ Wed, 22 Apr 2020 10:58:31: 7000000 INFO @ Wed, 22 Apr 2020 10:58:36: 4000000 INFO @ Wed, 22 Apr 2020 10:58:38: 8000000 INFO @ Wed, 22 Apr 2020 10:58:42: 5000000 INFO @ Wed, 22 Apr 2020 10:58:45: 9000000 INFO @ Wed, 22 Apr 2020 10:58:49: 6000000 INFO @ Wed, 22 Apr 2020 10:58:52: 10000000 INFO @ Wed, 22 Apr 2020 10:58:55: 7000000 INFO @ Wed, 22 Apr 2020 10:58:55: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:58:55: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:58:55: #1 total tags in treatment: 5093318 INFO @ Wed, 22 Apr 2020 10:58:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:58:55: #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 10:58:55: #1 tags after filtering in treatment: 4148492 INFO @ Wed, 22 Apr 2020 10:58:55: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 10:58:55: #1 finished! INFO @ Wed, 22 Apr 2020 10:58:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:58:56: #2 number of paired peaks: 44 WARNING @ Wed, 22 Apr 2020 10:58:56: Too few paired peaks (44) 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 10:58:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.10_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/SRX7409598/SRX7409598.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:59:01: 8000000 INFO @ Wed, 22 Apr 2020 10:59:07: 9000000 INFO @ Wed, 22 Apr 2020 10:59:13: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:59:16: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:59:16: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:59:16: #1 total tags in treatment: 5093318 INFO @ Wed, 22 Apr 2020 10:59:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:59:16: #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 10:59:16: #1 tags after filtering in treatment: 4148492 INFO @ Wed, 22 Apr 2020 10:59:16: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 10:59:16: #1 finished! INFO @ Wed, 22 Apr 2020 10:59:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:59:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:59:16: #2 number of paired peaks: 44 WARNING @ Wed, 22 Apr 2020 10:59:16: Too few paired peaks (44) 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 10:59:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.20_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/SRX7409598/SRX7409598.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409598/SRX7409598.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。