Job ID = 5791642 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:12:05 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 ) 2020-04-22T01:12:05 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 : 21,198,554 reads read : 42,397,108 reads written : 42,397,108 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: 00:10:46 21198554 reads; of these: 21198554 (100.00%) were paired; of these: 1022913 (4.83%) aligned concordantly 0 times 18446697 (87.02%) aligned concordantly exactly 1 time 1728944 (8.16%) aligned concordantly >1 times ---- 1022913 pairs aligned concordantly 0 times; of these: 19087 (1.87%) aligned discordantly 1 time ---- 1003826 pairs aligned 0 times concordantly or discordantly; of these: 2007652 mates make up the pairs; of these: 1782545 (88.79%) aligned 0 times 196438 (9.78%) aligned exactly 1 time 28669 (1.43%) aligned >1 times 95.80% overall alignment rate Time searching: 00:10:46 Overall time: 00:10:46 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 20 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] 3433221 / 20182166 = 0.1701 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 10:35:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.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 10:35:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:35:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:35:51: 1000000 INFO @ Wed, 22 Apr 2020 10:35:56: 2000000 INFO @ Wed, 22 Apr 2020 10:36:00: 3000000 INFO @ Wed, 22 Apr 2020 10:36:05: 4000000 INFO @ Wed, 22 Apr 2020 10:36:10: 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 10:36:15: 6000000 INFO @ Wed, 22 Apr 2020 10:36:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.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 10:36:16: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:36:16: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:36:20: 7000000 INFO @ Wed, 22 Apr 2020 10:36:23: 1000000 INFO @ Wed, 22 Apr 2020 10:36:26: 8000000 INFO @ Wed, 22 Apr 2020 10:36:29: 2000000 INFO @ Wed, 22 Apr 2020 10:36:32: 9000000 INFO @ Wed, 22 Apr 2020 10:36:35: 3000000 INFO @ Wed, 22 Apr 2020 10:36:37: 10000000 INFO @ Wed, 22 Apr 2020 10:36:42: 4000000 INFO @ Wed, 22 Apr 2020 10:36:43: 11000000 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 BedGraph に変換中... INFO @ Wed, 22 Apr 2020 10:36:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.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 10:36:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:36:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:36:49: 5000000 INFO @ Wed, 22 Apr 2020 10:36:49: 12000000 INFO @ Wed, 22 Apr 2020 10:36:52: 1000000 INFO @ Wed, 22 Apr 2020 10:36:55: 13000000 INFO @ Wed, 22 Apr 2020 10:36:56: 6000000 INFO @ Wed, 22 Apr 2020 10:36:58: 2000000 INFO @ Wed, 22 Apr 2020 10:37:01: 14000000 INFO @ Wed, 22 Apr 2020 10:37:03: 7000000 INFO @ Wed, 22 Apr 2020 10:37:04: 3000000 INFO @ Wed, 22 Apr 2020 10:37:07: 15000000 INFO @ Wed, 22 Apr 2020 10:37:10: 8000000 INFO @ Wed, 22 Apr 2020 10:37:10: 4000000 INFO @ Wed, 22 Apr 2020 10:37:13: 16000000 INFO @ Wed, 22 Apr 2020 10:37:16: 5000000 INFO @ Wed, 22 Apr 2020 10:37:17: 9000000 INFO @ Wed, 22 Apr 2020 10:37:19: 17000000 INFO @ Wed, 22 Apr 2020 10:37:22: 6000000 INFO @ Wed, 22 Apr 2020 10:37:23: 10000000 INFO @ Wed, 22 Apr 2020 10:37:25: 18000000 INFO @ Wed, 22 Apr 2020 10:37:28: 7000000 INFO @ Wed, 22 Apr 2020 10:37:30: 11000000 INFO @ Wed, 22 Apr 2020 10:37:31: 19000000 INFO @ Wed, 22 Apr 2020 10:37:35: 8000000 INFO @ Wed, 22 Apr 2020 10:37:36: 12000000 INFO @ Wed, 22 Apr 2020 10:37:37: 20000000 INFO @ Wed, 22 Apr 2020 10:37:41: 9000000 INFO @ Wed, 22 Apr 2020 10:37:42: 13000000 INFO @ Wed, 22 Apr 2020 10:37:43: 21000000 INFO @ Wed, 22 Apr 2020 10:37:46: 10000000 INFO @ Wed, 22 Apr 2020 10:37:49: 14000000 INFO @ Wed, 22 Apr 2020 10:37:49: 22000000 INFO @ Wed, 22 Apr 2020 10:37:52: 11000000 INFO @ Wed, 22 Apr 2020 10:37:55: 15000000 INFO @ Wed, 22 Apr 2020 10:37:55: 23000000 INFO @ Wed, 22 Apr 2020 10:37:58: 12000000 INFO @ Wed, 22 Apr 2020 10:38:01: 24000000 INFO @ Wed, 22 Apr 2020 10:38:02: 16000000 INFO @ Wed, 22 Apr 2020 10:38:04: 13000000 INFO @ Wed, 22 Apr 2020 10:38:07: 25000000 INFO @ Wed, 22 Apr 2020 10:38:08: 17000000 INFO @ Wed, 22 Apr 2020 10:38:10: 14000000 INFO @ Wed, 22 Apr 2020 10:38:13: 26000000 INFO @ Wed, 22 Apr 2020 10:38:15: 18000000 INFO @ Wed, 22 Apr 2020 10:38:16: 15000000 INFO @ Wed, 22 Apr 2020 10:38:19: 27000000 INFO @ Wed, 22 Apr 2020 10:38:21: 19000000 INFO @ Wed, 22 Apr 2020 10:38:22: 16000000 INFO @ Wed, 22 Apr 2020 10:38:25: 28000000 INFO @ Wed, 22 Apr 2020 10:38:28: 20000000 INFO @ Wed, 22 Apr 2020 10:38:28: 17000000 INFO @ Wed, 22 Apr 2020 10:38:30: 29000000 INFO @ Wed, 22 Apr 2020 10:38:34: 21000000 INFO @ Wed, 22 Apr 2020 10:38:34: 18000000 INFO @ Wed, 22 Apr 2020 10:38:36: 30000000 INFO @ Wed, 22 Apr 2020 10:38:40: 19000000 INFO @ Wed, 22 Apr 2020 10:38:41: 22000000 INFO @ Wed, 22 Apr 2020 10:38:42: 31000000 INFO @ Wed, 22 Apr 2020 10:38:46: 20000000 INFO @ Wed, 22 Apr 2020 10:38:47: 23000000 INFO @ Wed, 22 Apr 2020 10:38:48: 32000000 INFO @ Wed, 22 Apr 2020 10:38:52: 21000000 INFO @ Wed, 22 Apr 2020 10:38:53: 24000000 INFO @ Wed, 22 Apr 2020 10:38:54: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:38:58: 22000000 INFO @ Wed, 22 Apr 2020 10:38:59: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:38:59: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:38:59: #1 total tags in treatment: 16743475 INFO @ Wed, 22 Apr 2020 10:38:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:38:59: #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 10:38:59: #1 tags after filtering in treatment: 9879934 INFO @ Wed, 22 Apr 2020 10:38:59: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 10:38:59: #1 finished! INFO @ Wed, 22 Apr 2020 10:38:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:38:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:39:00: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:39:00: 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 10:39:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Wed, 22 Apr 2020 10:39:00: 25000000 rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:39:04: 23000000 INFO @ Wed, 22 Apr 2020 10:39:06: 26000000 INFO @ Wed, 22 Apr 2020 10:39:09: 24000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:39:12: 27000000 INFO @ Wed, 22 Apr 2020 10:39:15: 25000000 INFO @ Wed, 22 Apr 2020 10:39:19: 28000000 INFO @ Wed, 22 Apr 2020 10:39:21: 26000000 INFO @ Wed, 22 Apr 2020 10:39:25: 29000000 INFO @ Wed, 22 Apr 2020 10:39:26: 27000000 INFO @ Wed, 22 Apr 2020 10:39:31: 30000000 INFO @ Wed, 22 Apr 2020 10:39:32: 28000000 INFO @ Wed, 22 Apr 2020 10:39:37: 31000000 INFO @ Wed, 22 Apr 2020 10:39:38: 29000000 INFO @ Wed, 22 Apr 2020 10:39:44: 30000000 INFO @ Wed, 22 Apr 2020 10:39:44: 32000000 INFO @ Wed, 22 Apr 2020 10:39:49: 31000000 INFO @ Wed, 22 Apr 2020 10:39:50: 33000000 INFO @ Wed, 22 Apr 2020 10:39:55: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:39:55: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:39:55: #1 total tags in treatment: 16743475 INFO @ Wed, 22 Apr 2020 10:39:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:39:55: #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 10:39:55: 32000000 INFO @ Wed, 22 Apr 2020 10:39:55: #1 tags after filtering in treatment: 9879934 INFO @ Wed, 22 Apr 2020 10:39:55: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 10:39:55: #1 finished! INFO @ Wed, 22 Apr 2020 10:39:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:39:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:39:56: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:39:56: 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 10:39:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:40:00: 33000000 INFO @ Wed, 22 Apr 2020 10:40:05: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:40:05: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:40:05: #1 total tags in treatment: 16743475 INFO @ Wed, 22 Apr 2020 10:40:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:40:05: #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 10:40:05: #1 tags after filtering in treatment: 9879934 INFO @ Wed, 22 Apr 2020 10:40:05: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 10:40:05: #1 finished! INFO @ Wed, 22 Apr 2020 10:40:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:40:05: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:40:05: 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 10:40:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.20_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/SRX7409607/SRX7409607.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409607/SRX7409607.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling