Job ID = 5791484 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:28:32 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 ) 2020-04-22T00:35:25 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 ) 2020-04-22T00:41:27 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 ) 2020-04-22T00:41:27 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 ) 2020-04-22T00:41:27 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 : 32,257,521 reads read : 64,515,042 reads written : 64,515,042 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: 00:08:44 32257521 reads; of these: 32257521 (100.00%) were paired; of these: 16909595 (52.42%) aligned concordantly 0 times 13623301 (42.23%) aligned concordantly exactly 1 time 1724625 (5.35%) aligned concordantly >1 times ---- 16909595 pairs aligned concordantly 0 times; of these: 28332 (0.17%) aligned discordantly 1 time ---- 16881263 pairs aligned 0 times concordantly or discordantly; of these: 33762526 mates make up the pairs; of these: 33552938 (99.38%) aligned 0 times 173231 (0.51%) aligned exactly 1 time 36357 (0.11%) aligned >1 times 47.99% overall alignment rate Time searching: 00:08:44 Overall time: 00:08:44 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] 4692387 / 15360224 = 0.3055 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 10:03:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.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 10:03:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:03:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:03:09: 1000000 INFO @ Wed, 22 Apr 2020 10:03:14: 2000000 INFO @ Wed, 22 Apr 2020 10:03:18: 3000000 INFO @ Wed, 22 Apr 2020 10:03:23: 4000000 INFO @ Wed, 22 Apr 2020 10:03:27: 5000000 INFO @ Wed, 22 Apr 2020 10:03:32: 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 10:03:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.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 10:03:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:03:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:03:37: 7000000 INFO @ Wed, 22 Apr 2020 10:03:39: 1000000 INFO @ Wed, 22 Apr 2020 10:03:42: 8000000 INFO @ Wed, 22 Apr 2020 10:03:45: 2000000 INFO @ Wed, 22 Apr 2020 10:03:46: 9000000 INFO @ Wed, 22 Apr 2020 10:03:51: 3000000 INFO @ Wed, 22 Apr 2020 10:03:52: 10000000 INFO @ Wed, 22 Apr 2020 10:03:56: 4000000 INFO @ Wed, 22 Apr 2020 10:03:56: 11000000 INFO @ Wed, 22 Apr 2020 10:04:01: 12000000 INFO @ Wed, 22 Apr 2020 10:04:01: 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 10:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.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 10:04:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:04:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:04:06: 13000000 INFO @ Wed, 22 Apr 2020 10:04:07: 6000000 INFO @ Wed, 22 Apr 2020 10:04:09: 1000000 INFO @ Wed, 22 Apr 2020 10:04:12: 14000000 INFO @ Wed, 22 Apr 2020 10:04:12: 7000000 INFO @ Wed, 22 Apr 2020 10:04:15: 2000000 INFO @ Wed, 22 Apr 2020 10:04:17: 15000000 INFO @ Wed, 22 Apr 2020 10:04:17: 8000000 INFO @ Wed, 22 Apr 2020 10:04:20: 3000000 INFO @ Wed, 22 Apr 2020 10:04:23: 16000000 INFO @ Wed, 22 Apr 2020 10:04:23: 9000000 INFO @ Wed, 22 Apr 2020 10:04:26: 4000000 INFO @ Wed, 22 Apr 2020 10:04:28: 17000000 INFO @ Wed, 22 Apr 2020 10:04:28: 10000000 INFO @ Wed, 22 Apr 2020 10:04:31: 5000000 INFO @ Wed, 22 Apr 2020 10:04:33: 18000000 INFO @ Wed, 22 Apr 2020 10:04:34: 11000000 INFO @ Wed, 22 Apr 2020 10:04:36: 6000000 INFO @ Wed, 22 Apr 2020 10:04:39: 19000000 INFO @ Wed, 22 Apr 2020 10:04:39: 12000000 INFO @ Wed, 22 Apr 2020 10:04:42: 7000000 INFO @ Wed, 22 Apr 2020 10:04:44: 20000000 INFO @ Wed, 22 Apr 2020 10:04:45: 13000000 INFO @ Wed, 22 Apr 2020 10:04:47: 8000000 INFO @ Wed, 22 Apr 2020 10:04:49: 21000000 INFO @ Wed, 22 Apr 2020 10:04:51: 14000000 INFO @ Wed, 22 Apr 2020 10:04:52: 9000000 INFO @ Wed, 22 Apr 2020 10:04:52: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:04:52: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:04:52: #1 total tags in treatment: 10661207 INFO @ Wed, 22 Apr 2020 10:04:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:04:52: #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 10:04:53: #1 tags after filtering in treatment: 8009678 INFO @ Wed, 22 Apr 2020 10:04:53: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 22 Apr 2020 10:04:53: #1 finished! INFO @ Wed, 22 Apr 2020 10:04:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:04:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:04:53: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:04:53: 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 10:04:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.05_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/SRX7409572/SRX7409572.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:04:56: 15000000 INFO @ Wed, 22 Apr 2020 10:04:57: 10000000 INFO @ Wed, 22 Apr 2020 10:05:01: 16000000 INFO @ Wed, 22 Apr 2020 10:05:02: 11000000 INFO @ Wed, 22 Apr 2020 10:05:06: 17000000 INFO @ Wed, 22 Apr 2020 10:05:07: 12000000 INFO @ Wed, 22 Apr 2020 10:05:11: 18000000 INFO @ Wed, 22 Apr 2020 10:05:11: 13000000 INFO @ Wed, 22 Apr 2020 10:05:16: 14000000 INFO @ Wed, 22 Apr 2020 10:05:16: 19000000 INFO @ Wed, 22 Apr 2020 10:05:21: 15000000 INFO @ Wed, 22 Apr 2020 10:05:21: 20000000 INFO @ Wed, 22 Apr 2020 10:05:25: 16000000 INFO @ Wed, 22 Apr 2020 10:05:26: 21000000 INFO @ Wed, 22 Apr 2020 10:05:29: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:05:29: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:05:29: #1 total tags in treatment: 10661207 INFO @ Wed, 22 Apr 2020 10:05:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:05:29: #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 10:05:29: #1 tags after filtering in treatment: 8009678 INFO @ Wed, 22 Apr 2020 10:05:29: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 22 Apr 2020 10:05:29: #1 finished! INFO @ Wed, 22 Apr 2020 10:05:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:05:29: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:05:29: 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 10:05:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.10_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/SRX7409572/SRX7409572.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:05:30: 17000000 INFO @ Wed, 22 Apr 2020 10:05:34: 18000000 INFO @ Wed, 22 Apr 2020 10:05:39: 19000000 INFO @ Wed, 22 Apr 2020 10:05:43: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:05:48: 21000000 INFO @ Wed, 22 Apr 2020 10:05:51: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:05:51: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:05:51: #1 total tags in treatment: 10661207 INFO @ Wed, 22 Apr 2020 10:05:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:05:51: #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 10:05:51: #1 tags after filtering in treatment: 8009678 INFO @ Wed, 22 Apr 2020 10:05:51: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 22 Apr 2020 10:05:51: #1 finished! INFO @ Wed, 22 Apr 2020 10:05:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:05:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:05:51: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:05:51: 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 10:05:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.20_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/SRX7409572/SRX7409572.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409572/SRX7409572.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。