Job ID = 5791659 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:22:04 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 ) 2020-04-22T01:22:04 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 ) 2020-04-22T01:22:04 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 ) 2020-04-22T01:27:14 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 ) 2020-04-22T01:27:14 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 ) 2020-04-22T01:27:14 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 : 26,666,818 reads read : 53,333,636 reads written : 53,333,636 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: 00:14:50 26666818 reads; of these: 26666818 (100.00%) were paired; of these: 749731 (2.81%) aligned concordantly 0 times 23447512 (87.93%) aligned concordantly exactly 1 time 2469575 (9.26%) aligned concordantly >1 times ---- 749731 pairs aligned concordantly 0 times; of these: 29249 (3.90%) aligned discordantly 1 time ---- 720482 pairs aligned 0 times concordantly or discordantly; of these: 1440964 mates make up the pairs; of these: 1212961 (84.18%) aligned 0 times 190929 (13.25%) aligned exactly 1 time 37074 (2.57%) aligned >1 times 97.73% overall alignment rate Time searching: 00:14:50 Overall time: 00:14:50 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] 3870952 / 25926181 = 0.1493 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 10:52:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.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 10:52:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:52:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:53:05: 1000000 INFO @ Wed, 22 Apr 2020 10:53:11: 2000000 INFO @ Wed, 22 Apr 2020 10:53:17: 3000000 INFO @ Wed, 22 Apr 2020 10:53:23: 4000000 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 10:53:29: 5000000 INFO @ Wed, 22 Apr 2020 10:53:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.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 10:53:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:53:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:53:35: 6000000 INFO @ Wed, 22 Apr 2020 10:53:36: 1000000 INFO @ Wed, 22 Apr 2020 10:53:41: 7000000 INFO @ Wed, 22 Apr 2020 10:53:42: 2000000 INFO @ Wed, 22 Apr 2020 10:53:47: 8000000 INFO @ Wed, 22 Apr 2020 10:53:48: 3000000 INFO @ Wed, 22 Apr 2020 10:53:53: 9000000 INFO @ Wed, 22 Apr 2020 10:53:55: 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 10:53:59: 10000000 INFO @ Wed, 22 Apr 2020 10:53:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.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 10:53:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:53:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:54:01: 5000000 INFO @ Wed, 22 Apr 2020 10:54:05: 11000000 INFO @ Wed, 22 Apr 2020 10:54:05: 1000000 INFO @ Wed, 22 Apr 2020 10:54:08: 6000000 INFO @ Wed, 22 Apr 2020 10:54:11: 2000000 INFO @ Wed, 22 Apr 2020 10:54:11: 12000000 INFO @ Wed, 22 Apr 2020 10:54:14: 7000000 INFO @ Wed, 22 Apr 2020 10:54:17: 3000000 INFO @ Wed, 22 Apr 2020 10:54:18: 13000000 INFO @ Wed, 22 Apr 2020 10:54:21: 8000000 INFO @ Wed, 22 Apr 2020 10:54:23: 4000000 INFO @ Wed, 22 Apr 2020 10:54:24: 14000000 INFO @ Wed, 22 Apr 2020 10:54:27: 9000000 INFO @ Wed, 22 Apr 2020 10:54:29: 5000000 INFO @ Wed, 22 Apr 2020 10:54:31: 15000000 INFO @ Wed, 22 Apr 2020 10:54:32: 10000000 INFO @ Wed, 22 Apr 2020 10:54:34: 6000000 INFO @ Wed, 22 Apr 2020 10:54:37: 16000000 INFO @ Wed, 22 Apr 2020 10:54:39: 11000000 INFO @ Wed, 22 Apr 2020 10:54:40: 7000000 INFO @ Wed, 22 Apr 2020 10:54:43: 17000000 INFO @ Wed, 22 Apr 2020 10:54:45: 12000000 INFO @ Wed, 22 Apr 2020 10:54:46: 8000000 INFO @ Wed, 22 Apr 2020 10:54:49: 18000000 INFO @ Wed, 22 Apr 2020 10:54:52: 13000000 INFO @ Wed, 22 Apr 2020 10:54:52: 9000000 INFO @ Wed, 22 Apr 2020 10:54:56: 19000000 INFO @ Wed, 22 Apr 2020 10:54:58: 14000000 INFO @ Wed, 22 Apr 2020 10:54:58: 10000000 INFO @ Wed, 22 Apr 2020 10:55:04: 20000000 INFO @ Wed, 22 Apr 2020 10:55:04: 11000000 INFO @ Wed, 22 Apr 2020 10:55:05: 15000000 INFO @ Wed, 22 Apr 2020 10:55:10: 12000000 INFO @ Wed, 22 Apr 2020 10:55:11: 16000000 INFO @ Wed, 22 Apr 2020 10:55:13: 21000000 INFO @ Wed, 22 Apr 2020 10:55:16: 13000000 INFO @ Wed, 22 Apr 2020 10:55:17: 17000000 INFO @ Wed, 22 Apr 2020 10:55:20: 22000000 INFO @ Wed, 22 Apr 2020 10:55:21: 14000000 INFO @ Wed, 22 Apr 2020 10:55:23: 18000000 INFO @ Wed, 22 Apr 2020 10:55:26: 23000000 INFO @ Wed, 22 Apr 2020 10:55:27: 15000000 INFO @ Wed, 22 Apr 2020 10:55:30: 19000000 INFO @ Wed, 22 Apr 2020 10:55:33: 16000000 INFO @ Wed, 22 Apr 2020 10:55:33: 24000000 INFO @ Wed, 22 Apr 2020 10:55:36: 20000000 INFO @ Wed, 22 Apr 2020 10:55:39: 17000000 INFO @ Wed, 22 Apr 2020 10:55:39: 25000000 INFO @ Wed, 22 Apr 2020 10:55:43: 21000000 INFO @ Wed, 22 Apr 2020 10:55:45: 18000000 INFO @ Wed, 22 Apr 2020 10:55:46: 26000000 INFO @ Wed, 22 Apr 2020 10:55:48: 22000000 INFO @ Wed, 22 Apr 2020 10:55:50: 19000000 INFO @ Wed, 22 Apr 2020 10:55:52: 27000000 INFO @ Wed, 22 Apr 2020 10:55:55: 23000000 INFO @ Wed, 22 Apr 2020 10:55:56: 20000000 INFO @ Wed, 22 Apr 2020 10:55:59: 28000000 INFO @ Wed, 22 Apr 2020 10:56:01: 24000000 INFO @ Wed, 22 Apr 2020 10:56:02: 21000000 INFO @ Wed, 22 Apr 2020 10:56:04: 29000000 INFO @ Wed, 22 Apr 2020 10:56:07: 25000000 INFO @ Wed, 22 Apr 2020 10:56:08: 22000000 INFO @ Wed, 22 Apr 2020 10:56:10: 30000000 INFO @ Wed, 22 Apr 2020 10:56:13: 26000000 INFO @ Wed, 22 Apr 2020 10:56:14: 23000000 INFO @ Wed, 22 Apr 2020 10:56:16: 31000000 INFO @ Wed, 22 Apr 2020 10:56:20: 27000000 INFO @ Wed, 22 Apr 2020 10:56:20: 24000000 INFO @ Wed, 22 Apr 2020 10:56:22: 32000000 INFO @ Wed, 22 Apr 2020 10:56:26: 28000000 INFO @ Wed, 22 Apr 2020 10:56:26: 25000000 INFO @ Wed, 22 Apr 2020 10:56:29: 33000000 INFO @ Wed, 22 Apr 2020 10:56:31: 26000000 INFO @ Wed, 22 Apr 2020 10:56:32: 29000000 INFO @ Wed, 22 Apr 2020 10:56:35: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:56:37: 30000000 INFO @ Wed, 22 Apr 2020 10:56:37: 27000000 INFO @ Wed, 22 Apr 2020 10:56:41: 35000000 INFO @ Wed, 22 Apr 2020 10:56:43: 28000000 INFO @ Wed, 22 Apr 2020 10:56:44: 31000000 INFO @ Wed, 22 Apr 2020 10:56:48: 36000000 INFO @ Wed, 22 Apr 2020 10:56:49: 29000000 INFO @ Wed, 22 Apr 2020 10:56:50: 32000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:56:55: 37000000 INFO @ Wed, 22 Apr 2020 10:56:56: 30000000 INFO @ Wed, 22 Apr 2020 10:56:57: 33000000 INFO @ Wed, 22 Apr 2020 10:57:01: 38000000 INFO @ Wed, 22 Apr 2020 10:57:02: 31000000 INFO @ Wed, 22 Apr 2020 10:57:03: 34000000 INFO @ Wed, 22 Apr 2020 10:57:08: 39000000 INFO @ Wed, 22 Apr 2020 10:57:08: 32000000 INFO @ Wed, 22 Apr 2020 10:57:10: 35000000 INFO @ Wed, 22 Apr 2020 10:57:14: 33000000 INFO @ Wed, 22 Apr 2020 10:57:14: 40000000 INFO @ Wed, 22 Apr 2020 10:57:16: 36000000 INFO @ Wed, 22 Apr 2020 10:57:20: 34000000 INFO @ Wed, 22 Apr 2020 10:57:21: 41000000 INFO @ Wed, 22 Apr 2020 10:57:23: 37000000 INFO @ Wed, 22 Apr 2020 10:57:25: 35000000 INFO @ Wed, 22 Apr 2020 10:57:27: 42000000 INFO @ Wed, 22 Apr 2020 10:57:29: 38000000 INFO @ Wed, 22 Apr 2020 10:57:31: 36000000 INFO @ Wed, 22 Apr 2020 10:57:33: 43000000 INFO @ Wed, 22 Apr 2020 10:57:36: 39000000 INFO @ Wed, 22 Apr 2020 10:57:37: 37000000 INFO @ Wed, 22 Apr 2020 10:57:40: 44000000 INFO @ Wed, 22 Apr 2020 10:57:42: 40000000 INFO @ Wed, 22 Apr 2020 10:57:42: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:57:42: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:57:42: #1 total tags in treatment: 22047624 INFO @ Wed, 22 Apr 2020 10:57:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:57:42: #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 10:57:42: #1 tags after filtering in treatment: 12098465 INFO @ Wed, 22 Apr 2020 10:57:42: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Apr 2020 10:57:42: #1 finished! INFO @ Wed, 22 Apr 2020 10:57:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:57:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:57:43: 38000000 INFO @ Wed, 22 Apr 2020 10:57:43: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:57:43: 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 10:57:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.05_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/SRX7409622/SRX7409622.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:57:48: 41000000 INFO @ Wed, 22 Apr 2020 10:57:49: 39000000 INFO @ Wed, 22 Apr 2020 10:57:54: 42000000 INFO @ Wed, 22 Apr 2020 10:57:54: 40000000 INFO @ Wed, 22 Apr 2020 10:58:00: 43000000 INFO @ Wed, 22 Apr 2020 10:58:00: 41000000 INFO @ Wed, 22 Apr 2020 10:58:06: 44000000 INFO @ Wed, 22 Apr 2020 10:58:06: 42000000 INFO @ Wed, 22 Apr 2020 10:58:08: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:58:08: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:58:08: #1 total tags in treatment: 22047624 INFO @ Wed, 22 Apr 2020 10:58:08: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:58:08: #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 10:58:08: #1 tags after filtering in treatment: 12098465 INFO @ Wed, 22 Apr 2020 10:58:08: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Apr 2020 10:58:08: #1 finished! INFO @ Wed, 22 Apr 2020 10:58:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:58:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:58:09: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:58:09: 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 10:58:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.10_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/SRX7409622/SRX7409622.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:58:11: 43000000 INFO @ Wed, 22 Apr 2020 10:58:16: 44000000 INFO @ Wed, 22 Apr 2020 10:58:19: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:58:19: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:58:19: #1 total tags in treatment: 22047624 INFO @ Wed, 22 Apr 2020 10:58:19: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:58:19: #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 10:58:19: #1 tags after filtering in treatment: 12098465 INFO @ Wed, 22 Apr 2020 10:58:19: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Apr 2020 10:58:19: #1 finished! INFO @ Wed, 22 Apr 2020 10:58:19: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:58:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:58:20: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:58:20: 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 10:58:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.20_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/SRX7409622/SRX7409622.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409622/SRX7409622.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling