Job ID = 5791622 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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 ) 2020-04-22T00:50:48 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 ) 2020-04-22T00:52:20 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 ) 2020-04-22T00:52:20 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 ) spots read : 32,610,608 reads read : 65,221,216 reads written : 65,221,216 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: 00:09:51 32610608 reads; of these: 32610608 (100.00%) were paired; of these: 15044918 (46.14%) aligned concordantly 0 times 15845029 (48.59%) aligned concordantly exactly 1 time 1720661 (5.28%) aligned concordantly >1 times ---- 15044918 pairs aligned concordantly 0 times; of these: 38925 (0.26%) aligned discordantly 1 time ---- 15005993 pairs aligned 0 times concordantly or discordantly; of these: 30011986 mates make up the pairs; of these: 29600093 (98.63%) aligned 0 times 358868 (1.20%) aligned exactly 1 time 53025 (0.18%) aligned >1 times 54.62% overall alignment rate Time searching: 00:09:51 Overall time: 00:09:51 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] 10297718 / 17575337 = 0.5859 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 10:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.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 10:18:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:18:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:18:42: 1000000 INFO @ Wed, 22 Apr 2020 10:18:46: 2000000 INFO @ Wed, 22 Apr 2020 10:18:51: 3000000 INFO @ Wed, 22 Apr 2020 10:18:55: 4000000 INFO @ Wed, 22 Apr 2020 10:19:00: 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 10:19:04: 6000000 INFO @ Wed, 22 Apr 2020 10:19:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.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 10:19:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:19:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:19:09: 7000000 INFO @ Wed, 22 Apr 2020 10:19:13: 1000000 INFO @ Wed, 22 Apr 2020 10:19:14: 8000000 INFO @ Wed, 22 Apr 2020 10:19:18: 2000000 INFO @ Wed, 22 Apr 2020 10:19:19: 9000000 INFO @ Wed, 22 Apr 2020 10:19:24: 10000000 INFO @ Wed, 22 Apr 2020 10:19:24: 3000000 INFO @ Wed, 22 Apr 2020 10:19:29: 11000000 INFO @ Wed, 22 Apr 2020 10:19:30: 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 10:19:34: 12000000 INFO @ Wed, 22 Apr 2020 10:19:36: 5000000 INFO @ Wed, 22 Apr 2020 10:19:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.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 10:19:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:19:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:19:39: 13000000 INFO @ Wed, 22 Apr 2020 10:19:41: 1000000 INFO @ Wed, 22 Apr 2020 10:19:42: 6000000 INFO @ Wed, 22 Apr 2020 10:19:44: 14000000 INFO @ Wed, 22 Apr 2020 10:19:46: 2000000 INFO @ Wed, 22 Apr 2020 10:19:48: 7000000 INFO @ Wed, 22 Apr 2020 10:19:49: 15000000 INFO @ Wed, 22 Apr 2020 10:19:50: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:19:50: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:19:50: #1 total tags in treatment: 7273094 INFO @ Wed, 22 Apr 2020 10:19:50: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:19:50: #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 10:19:50: #1 tags after filtering in treatment: 5935872 INFO @ Wed, 22 Apr 2020 10:19:50: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 10:19:50: #1 finished! INFO @ Wed, 22 Apr 2020 10:19:50: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:19:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:19:50: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:19:50: 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 10:19:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.05_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/SRX7409590/SRX7409590.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:19:52: 3000000 INFO @ Wed, 22 Apr 2020 10:19:54: 8000000 INFO @ Wed, 22 Apr 2020 10:19:57: 4000000 INFO @ Wed, 22 Apr 2020 10:20:00: 9000000 INFO @ Wed, 22 Apr 2020 10:20:02: 5000000 INFO @ Wed, 22 Apr 2020 10:20:05: 10000000 INFO @ Wed, 22 Apr 2020 10:20:07: 6000000 INFO @ Wed, 22 Apr 2020 10:20:11: 11000000 INFO @ Wed, 22 Apr 2020 10:20:12: 7000000 INFO @ Wed, 22 Apr 2020 10:20:17: 12000000 INFO @ Wed, 22 Apr 2020 10:20:17: 8000000 INFO @ Wed, 22 Apr 2020 10:20:22: 13000000 INFO @ Wed, 22 Apr 2020 10:20:23: 9000000 INFO @ Wed, 22 Apr 2020 10:20:28: 10000000 INFO @ Wed, 22 Apr 2020 10:20:28: 14000000 INFO @ Wed, 22 Apr 2020 10:20:33: 11000000 INFO @ Wed, 22 Apr 2020 10:20:34: 15000000 INFO @ Wed, 22 Apr 2020 10:20:34: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:20:34: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:20:34: #1 total tags in treatment: 7273094 INFO @ Wed, 22 Apr 2020 10:20:34: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:20:34: #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 10:20:34: #1 tags after filtering in treatment: 5935872 INFO @ Wed, 22 Apr 2020 10:20:34: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 10:20:34: #1 finished! INFO @ Wed, 22 Apr 2020 10:20:34: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:20:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:20:34: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:20:34: 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 10:20:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.10_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/SRX7409590/SRX7409590.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:20:38: 12000000 INFO @ Wed, 22 Apr 2020 10:20:43: 13000000 INFO @ Wed, 22 Apr 2020 10:20:48: 14000000 INFO @ Wed, 22 Apr 2020 10:20:52: 15000000 INFO @ Wed, 22 Apr 2020 10:20:52: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:20:52: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:20:52: #1 total tags in treatment: 7273094 INFO @ Wed, 22 Apr 2020 10:20:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:20:52: #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 10:20:53: #1 tags after filtering in treatment: 5935872 INFO @ Wed, 22 Apr 2020 10:20:53: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 10:20:53: #1 finished! INFO @ Wed, 22 Apr 2020 10:20:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:20:53: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:20:53: 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 10:20:53: Process for pairing-model is terminated! BedGraph に変換しました。 BigWig に変換中... cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.20_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/SRX7409590/SRX7409590.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409590/SRX7409590.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。