Job ID = 5791641 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:58:30 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 ) 2020-04-22T00:58:30 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 ) 2020-04-22T01:01:18 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 ) 2020-04-22T01:01:18 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 ) 2020-04-22T01:03:25 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 ) 2020-04-22T01:12:05 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 : 23,325,518 reads read : 46,651,036 reads written : 46,651,036 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: 00:12:01 23325518 reads; of these: 23325518 (100.00%) were paired; of these: 683803 (2.93%) aligned concordantly 0 times 20647664 (88.52%) aligned concordantly exactly 1 time 1994051 (8.55%) aligned concordantly >1 times ---- 683803 pairs aligned concordantly 0 times; of these: 30148 (4.41%) aligned discordantly 1 time ---- 653655 pairs aligned 0 times concordantly or discordantly; of these: 1307310 mates make up the pairs; of these: 1031159 (78.88%) aligned 0 times 241081 (18.44%) aligned exactly 1 time 35070 (2.68%) aligned >1 times 97.79% overall alignment rate Time searching: 00:12:01 Overall time: 00:12:01 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] 3510234 / 22649744 = 0.1550 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 10:38:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.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 10:38:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:38:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:38:43: 1000000 INFO @ Wed, 22 Apr 2020 10:38:48: 2000000 INFO @ Wed, 22 Apr 2020 10:38:53: 3000000 INFO @ Wed, 22 Apr 2020 10:38:59: 4000000 INFO @ Wed, 22 Apr 2020 10:39:04: 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 10:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.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 10:39:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:39:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:39:09: 6000000 INFO @ Wed, 22 Apr 2020 10:39:13: 1000000 INFO @ Wed, 22 Apr 2020 10:39:15: 7000000 INFO @ Wed, 22 Apr 2020 10:39:18: 2000000 INFO @ Wed, 22 Apr 2020 10:39:20: 8000000 INFO @ Wed, 22 Apr 2020 10:39:23: 3000000 INFO @ Wed, 22 Apr 2020 10:39:26: 9000000 INFO @ Wed, 22 Apr 2020 10:39:29: 4000000 INFO @ Wed, 22 Apr 2020 10:39:31: 10000000 INFO @ Wed, 22 Apr 2020 10:39:34: 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 10:39:36: 11000000 INFO @ Wed, 22 Apr 2020 10:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.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 10:39:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:39:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:39:40: 6000000 INFO @ Wed, 22 Apr 2020 10:39:42: 12000000 INFO @ Wed, 22 Apr 2020 10:39:43: 1000000 INFO @ Wed, 22 Apr 2020 10:39:45: 7000000 INFO @ Wed, 22 Apr 2020 10:39:47: 13000000 INFO @ Wed, 22 Apr 2020 10:39:48: 2000000 INFO @ Wed, 22 Apr 2020 10:39:51: 8000000 INFO @ Wed, 22 Apr 2020 10:39:53: 14000000 INFO @ Wed, 22 Apr 2020 10:39:54: 3000000 INFO @ Wed, 22 Apr 2020 10:39:56: 9000000 INFO @ Wed, 22 Apr 2020 10:39:58: 15000000 INFO @ Wed, 22 Apr 2020 10:39:59: 4000000 INFO @ Wed, 22 Apr 2020 10:40:02: 10000000 INFO @ Wed, 22 Apr 2020 10:40:04: 16000000 INFO @ Wed, 22 Apr 2020 10:40:05: 5000000 INFO @ Wed, 22 Apr 2020 10:40:07: 11000000 INFO @ Wed, 22 Apr 2020 10:40:09: 17000000 INFO @ Wed, 22 Apr 2020 10:40:10: 6000000 INFO @ Wed, 22 Apr 2020 10:40:12: 12000000 INFO @ Wed, 22 Apr 2020 10:40:15: 18000000 INFO @ Wed, 22 Apr 2020 10:40:16: 7000000 INFO @ Wed, 22 Apr 2020 10:40:18: 13000000 INFO @ Wed, 22 Apr 2020 10:40:20: 19000000 INFO @ Wed, 22 Apr 2020 10:40:21: 8000000 INFO @ Wed, 22 Apr 2020 10:40:23: 14000000 INFO @ Wed, 22 Apr 2020 10:40:26: 20000000 INFO @ Wed, 22 Apr 2020 10:40:27: 9000000 INFO @ Wed, 22 Apr 2020 10:40:29: 15000000 INFO @ Wed, 22 Apr 2020 10:40:31: 21000000 INFO @ Wed, 22 Apr 2020 10:40:32: 10000000 INFO @ Wed, 22 Apr 2020 10:40:34: 16000000 INFO @ Wed, 22 Apr 2020 10:40:37: 22000000 INFO @ Wed, 22 Apr 2020 10:40:38: 11000000 INFO @ Wed, 22 Apr 2020 10:40:40: 17000000 INFO @ Wed, 22 Apr 2020 10:40:42: 23000000 INFO @ Wed, 22 Apr 2020 10:40:43: 12000000 INFO @ Wed, 22 Apr 2020 10:40:46: 18000000 INFO @ Wed, 22 Apr 2020 10:40:48: 24000000 INFO @ Wed, 22 Apr 2020 10:40:49: 13000000 INFO @ Wed, 22 Apr 2020 10:40:51: 19000000 INFO @ Wed, 22 Apr 2020 10:40:53: 25000000 INFO @ Wed, 22 Apr 2020 10:40:54: 14000000 INFO @ Wed, 22 Apr 2020 10:40:56: 20000000 INFO @ Wed, 22 Apr 2020 10:40:58: 26000000 INFO @ Wed, 22 Apr 2020 10:41:00: 15000000 INFO @ Wed, 22 Apr 2020 10:41:02: 21000000 INFO @ Wed, 22 Apr 2020 10:41:04: 27000000 INFO @ Wed, 22 Apr 2020 10:41:05: 16000000 INFO @ Wed, 22 Apr 2020 10:41:07: 22000000 INFO @ Wed, 22 Apr 2020 10:41:09: 28000000 INFO @ Wed, 22 Apr 2020 10:41:11: 17000000 INFO @ Wed, 22 Apr 2020 10:41:13: 23000000 INFO @ Wed, 22 Apr 2020 10:41:15: 29000000 INFO @ Wed, 22 Apr 2020 10:41:16: 18000000 INFO @ Wed, 22 Apr 2020 10:41:18: 24000000 INFO @ Wed, 22 Apr 2020 10:41:20: 30000000 INFO @ Wed, 22 Apr 2020 10:41:22: 19000000 INFO @ Wed, 22 Apr 2020 10:41:24: 25000000 INFO @ Wed, 22 Apr 2020 10:41:26: 31000000 INFO @ Wed, 22 Apr 2020 10:41:27: 20000000 INFO @ Wed, 22 Apr 2020 10:41:29: 26000000 INFO @ Wed, 22 Apr 2020 10:41:31: 32000000 INFO @ Wed, 22 Apr 2020 10:41:33: 21000000 INFO @ Wed, 22 Apr 2020 10:41:35: 27000000 INFO @ Wed, 22 Apr 2020 10:41:37: 33000000 INFO @ Wed, 22 Apr 2020 10:41:38: 22000000 INFO @ Wed, 22 Apr 2020 10:41:40: 28000000 INFO @ Wed, 22 Apr 2020 10:41:42: 34000000 INFO @ Wed, 22 Apr 2020 10:41:43: 23000000 INFO @ Wed, 22 Apr 2020 10:41:46: 29000000 INFO @ Wed, 22 Apr 2020 10:41:48: 35000000 INFO @ Wed, 22 Apr 2020 10:41:49: 24000000 INFO @ Wed, 22 Apr 2020 10:41:51: 30000000 INFO @ Wed, 22 Apr 2020 10:41:53: 36000000 INFO @ Wed, 22 Apr 2020 10:41:54: 25000000 INFO @ Wed, 22 Apr 2020 10:41:56: 31000000 INFO @ Wed, 22 Apr 2020 10:41:59: 37000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:42:00: 26000000 INFO @ Wed, 22 Apr 2020 10:42:02: 32000000 INFO @ Wed, 22 Apr 2020 10:42:04: 38000000 INFO @ Wed, 22 Apr 2020 10:42:05: 27000000 INFO @ Wed, 22 Apr 2020 10:42:07: 33000000 INFO @ Wed, 22 Apr 2020 10:42:07: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:42:07: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:42:07: #1 total tags in treatment: 19132732 INFO @ Wed, 22 Apr 2020 10:42:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:42:07: #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 10:42:08: #1 tags after filtering in treatment: 10875015 INFO @ Wed, 22 Apr 2020 10:42:08: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 10:42:08: #1 finished! INFO @ Wed, 22 Apr 2020 10:42:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:42:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:42:08: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:42:08: 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 10:42:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.05_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/SRX7409606/SRX7409606.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:42:11: 28000000 INFO @ Wed, 22 Apr 2020 10:42:13: 34000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:42:16: 29000000 INFO @ Wed, 22 Apr 2020 10:42:18: 35000000 INFO @ Wed, 22 Apr 2020 10:42:22: 30000000 INFO @ Wed, 22 Apr 2020 10:42:24: 36000000 INFO @ Wed, 22 Apr 2020 10:42:27: 31000000 INFO @ Wed, 22 Apr 2020 10:42:29: 37000000 INFO @ Wed, 22 Apr 2020 10:42:33: 32000000 INFO @ Wed, 22 Apr 2020 10:42:34: 38000000 INFO @ Wed, 22 Apr 2020 10:42:38: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:42:38: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:42:38: #1 total tags in treatment: 19132732 INFO @ Wed, 22 Apr 2020 10:42:38: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:42:38: #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 10:42:38: #1 tags after filtering in treatment: 10875015 INFO @ Wed, 22 Apr 2020 10:42:38: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 10:42:38: #1 finished! INFO @ Wed, 22 Apr 2020 10:42:38: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:42:38: 33000000 INFO @ Wed, 22 Apr 2020 10:42:39: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:42:39: 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 10:42:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.10_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/SRX7409606/SRX7409606.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:42:43: 34000000 INFO @ Wed, 22 Apr 2020 10:42:49: 35000000 INFO @ Wed, 22 Apr 2020 10:42:54: 36000000 INFO @ Wed, 22 Apr 2020 10:42:59: 37000000 INFO @ Wed, 22 Apr 2020 10:43:04: 38000000 INFO @ Wed, 22 Apr 2020 10:43:07: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:43:07: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:43:07: #1 total tags in treatment: 19132732 INFO @ Wed, 22 Apr 2020 10:43:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:43:07: #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 10:43:07: #1 tags after filtering in treatment: 10875015 INFO @ Wed, 22 Apr 2020 10:43:07: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 10:43:07: #1 finished! INFO @ Wed, 22 Apr 2020 10:43:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:43:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:43:08: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:43:08: 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 10:43:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.20_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/SRX7409606/SRX7409606.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409606/SRX7409606.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling