Job ID = 5791628 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:41:56 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 ) 2020-04-22T00:41:56 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 ) 2020-04-22T00:41:56 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 ) 2020-04-22T00:41:56 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 ) 2020-04-22T00:41:56 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 ) 2020-04-22T00:54:14 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T00:54:14 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T00:55:23 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 : 29,962,926 reads read : 59,925,852 reads written : 59,925,852 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: 00:15:08 29962926 reads; of these: 29962926 (100.00%) were paired; of these: 1964344 (6.56%) aligned concordantly 0 times 24966164 (83.32%) aligned concordantly exactly 1 time 3032418 (10.12%) aligned concordantly >1 times ---- 1964344 pairs aligned concordantly 0 times; of these: 45331 (2.31%) aligned discordantly 1 time ---- 1919013 pairs aligned 0 times concordantly or discordantly; of these: 3838026 mates make up the pairs; of these: 3575148 (93.15%) aligned 0 times 214214 (5.58%) aligned exactly 1 time 48664 (1.27%) aligned >1 times 94.03% overall alignment rate Time searching: 00:15:08 Overall time: 00:15:08 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 24 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] 16916858 / 28005274 = 0.6041 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 10:26:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.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 10:26:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:26:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:27:01: 1000000 INFO @ Wed, 22 Apr 2020 10:27:05: 2000000 INFO @ Wed, 22 Apr 2020 10:27:10: 3000000 INFO @ Wed, 22 Apr 2020 10:27:15: 4000000 INFO @ Wed, 22 Apr 2020 10:27:20: 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 10:27:25: 6000000 INFO @ Wed, 22 Apr 2020 10:27:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.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 10:27:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:27:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:27:29: 7000000 INFO @ Wed, 22 Apr 2020 10:27:31: 1000000 INFO @ Wed, 22 Apr 2020 10:27:34: 8000000 INFO @ Wed, 22 Apr 2020 10:27:36: 2000000 INFO @ Wed, 22 Apr 2020 10:27:39: 9000000 INFO @ Wed, 22 Apr 2020 10:27:41: 3000000 INFO @ Wed, 22 Apr 2020 10:27:43: 10000000 INFO @ Wed, 22 Apr 2020 10:27:46: 4000000 INFO @ Wed, 22 Apr 2020 10:27:48: 11000000 INFO @ Wed, 22 Apr 2020 10:27:51: 5000000 INFO @ Wed, 22 Apr 2020 10:27:53: 12000000 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 10:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.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 10:27:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:27:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:27:56: 6000000 INFO @ Wed, 22 Apr 2020 10:27:57: 13000000 INFO @ Wed, 22 Apr 2020 10:28:01: 1000000 INFO @ Wed, 22 Apr 2020 10:28:01: 7000000 INFO @ Wed, 22 Apr 2020 10:28:02: 14000000 INFO @ Wed, 22 Apr 2020 10:28:06: 8000000 INFO @ Wed, 22 Apr 2020 10:28:06: 2000000 INFO @ Wed, 22 Apr 2020 10:28:07: 15000000 INFO @ Wed, 22 Apr 2020 10:28:11: 16000000 INFO @ Wed, 22 Apr 2020 10:28:11: 9000000 INFO @ Wed, 22 Apr 2020 10:28:12: 3000000 INFO @ Wed, 22 Apr 2020 10:28:16: 17000000 INFO @ Wed, 22 Apr 2020 10:28:16: 10000000 INFO @ Wed, 22 Apr 2020 10:28:17: 4000000 INFO @ Wed, 22 Apr 2020 10:28:20: 18000000 INFO @ Wed, 22 Apr 2020 10:28:21: 11000000 INFO @ Wed, 22 Apr 2020 10:28:22: 5000000 INFO @ Wed, 22 Apr 2020 10:28:25: 19000000 INFO @ Wed, 22 Apr 2020 10:28:26: 12000000 INFO @ Wed, 22 Apr 2020 10:28:27: 6000000 INFO @ Wed, 22 Apr 2020 10:28:30: 20000000 INFO @ Wed, 22 Apr 2020 10:28:31: 13000000 INFO @ Wed, 22 Apr 2020 10:28:32: 7000000 INFO @ Wed, 22 Apr 2020 10:28:34: 21000000 INFO @ Wed, 22 Apr 2020 10:28:36: 14000000 INFO @ Wed, 22 Apr 2020 10:28:38: 8000000 INFO @ Wed, 22 Apr 2020 10:28:39: 22000000 INFO @ Wed, 22 Apr 2020 10:28:41: 15000000 INFO @ Wed, 22 Apr 2020 10:28:41: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:28:41: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:28:41: #1 total tags in treatment: 11084802 INFO @ Wed, 22 Apr 2020 10:28:41: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:28:41: #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 10:28:41: #1 tags after filtering in treatment: 8131818 INFO @ Wed, 22 Apr 2020 10:28:41: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 22 Apr 2020 10:28:41: #1 finished! INFO @ Wed, 22 Apr 2020 10:28:41: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:28:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:28:42: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:28:42: 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 10:28:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:28:43: 9000000 INFO @ Wed, 22 Apr 2020 10:28:46: 16000000 INFO @ Wed, 22 Apr 2020 10:28:48: 10000000 INFO @ Wed, 22 Apr 2020 10:28:51: 17000000 INFO @ Wed, 22 Apr 2020 10:28:53: 11000000 INFO @ Wed, 22 Apr 2020 10:28:56: 18000000 INFO @ Wed, 22 Apr 2020 10:28:57: 12000000 INFO @ Wed, 22 Apr 2020 10:29:00: 19000000 INFO @ Wed, 22 Apr 2020 10:29:02: 13000000 INFO @ Wed, 22 Apr 2020 10:29:05: 20000000 INFO @ Wed, 22 Apr 2020 10:29:06: 14000000 INFO @ Wed, 22 Apr 2020 10:29:09: 21000000 INFO @ Wed, 22 Apr 2020 10:29:11: 15000000 INFO @ Wed, 22 Apr 2020 10:29:14: 22000000 INFO @ Wed, 22 Apr 2020 10:29:16: 16000000 INFO @ Wed, 22 Apr 2020 10:29:17: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:29:17: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:29:17: #1 total tags in treatment: 11084802 INFO @ Wed, 22 Apr 2020 10:29:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:29:17: #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 10:29:17: #1 tags after filtering in treatment: 8131818 INFO @ Wed, 22 Apr 2020 10:29:17: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 22 Apr 2020 10:29:17: #1 finished! INFO @ Wed, 22 Apr 2020 10:29:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:29:17: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:29:17: 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 10:29:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.10_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/SRX7409596/SRX7409596.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:29:21: 17000000 INFO @ Wed, 22 Apr 2020 10:29:25: 18000000 INFO @ Wed, 22 Apr 2020 10:29:31: 19000000 INFO @ Wed, 22 Apr 2020 10:29:35: 20000000 INFO @ Wed, 22 Apr 2020 10:29:40: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:29:45: 22000000 INFO @ Wed, 22 Apr 2020 10:29:48: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:29:48: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:29:48: #1 total tags in treatment: 11084802 INFO @ Wed, 22 Apr 2020 10:29:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:29:48: #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 10:29:48: #1 tags after filtering in treatment: 8131818 INFO @ Wed, 22 Apr 2020 10:29:48: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 22 Apr 2020 10:29:48: #1 finished! INFO @ Wed, 22 Apr 2020 10:29:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:29:48: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:29:48: 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 10:29:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.20_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/SRX7409596/SRX7409596.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409596/SRX7409596.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。