Job ID = 5791310 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:28:08 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 ) 2020-04-22T00:28:08 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 ) 2020-04-22T00:28:08 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 ) 2020-04-22T00:28:08 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 ) 2020-04-22T00:36:22 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 ) 2020-04-22T00:36:22 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 ) 2020-04-22T00:41:05 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 : 31,637,841 reads read : 63,275,682 reads written : 63,275,682 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: 00:16:51 31637841 reads; of these: 31637841 (100.00%) were paired; of these: 304391 (0.96%) aligned concordantly 0 times 26744879 (84.53%) aligned concordantly exactly 1 time 4588571 (14.50%) aligned concordantly >1 times ---- 304391 pairs aligned concordantly 0 times; of these: 68263 (22.43%) aligned discordantly 1 time ---- 236128 pairs aligned 0 times concordantly or discordantly; of these: 472256 mates make up the pairs; of these: 284615 (60.27%) aligned 0 times 128939 (27.30%) aligned exactly 1 time 58702 (12.43%) aligned >1 times 99.55% overall alignment rate Time searching: 00:16:51 Overall time: 00:16:51 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 28 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] 9123520 / 31343237 = 0.2911 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 10:13:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.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 10:13:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:13:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:14:00: 1000000 INFO @ Wed, 22 Apr 2020 10:14:05: 2000000 INFO @ Wed, 22 Apr 2020 10:14:10: 3000000 INFO @ Wed, 22 Apr 2020 10:14:15: 4000000 INFO @ Wed, 22 Apr 2020 10:14:20: 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 10:14:25: 6000000 INFO @ Wed, 22 Apr 2020 10:14:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.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 10:14:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:14:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:14:31: 7000000 INFO @ Wed, 22 Apr 2020 10:14:32: 1000000 INFO @ Wed, 22 Apr 2020 10:14:37: 8000000 INFO @ Wed, 22 Apr 2020 10:14:37: 2000000 INFO @ Wed, 22 Apr 2020 10:14:42: 9000000 INFO @ Wed, 22 Apr 2020 10:14:43: 3000000 INFO @ Wed, 22 Apr 2020 10:14:48: 10000000 INFO @ Wed, 22 Apr 2020 10:14:49: 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 10:14:54: 11000000 INFO @ Wed, 22 Apr 2020 10:14:54: 5000000 INFO @ Wed, 22 Apr 2020 10:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.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 10:14:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:14:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:14:59: 12000000 INFO @ Wed, 22 Apr 2020 10:15:00: 6000000 INFO @ Wed, 22 Apr 2020 10:15:02: 1000000 INFO @ Wed, 22 Apr 2020 10:15:05: 13000000 INFO @ Wed, 22 Apr 2020 10:15:06: 7000000 INFO @ Wed, 22 Apr 2020 10:15:08: 2000000 INFO @ Wed, 22 Apr 2020 10:15:11: 14000000 INFO @ Wed, 22 Apr 2020 10:15:11: 8000000 INFO @ Wed, 22 Apr 2020 10:15:14: 3000000 INFO @ Wed, 22 Apr 2020 10:15:16: 15000000 INFO @ Wed, 22 Apr 2020 10:15:17: 9000000 INFO @ Wed, 22 Apr 2020 10:15:19: 4000000 INFO @ Wed, 22 Apr 2020 10:15:22: 16000000 INFO @ Wed, 22 Apr 2020 10:15:23: 10000000 INFO @ Wed, 22 Apr 2020 10:15:25: 5000000 INFO @ Wed, 22 Apr 2020 10:15:27: 17000000 INFO @ Wed, 22 Apr 2020 10:15:29: 11000000 INFO @ Wed, 22 Apr 2020 10:15:31: 6000000 INFO @ Wed, 22 Apr 2020 10:15:33: 18000000 INFO @ Wed, 22 Apr 2020 10:15:34: 12000000 INFO @ Wed, 22 Apr 2020 10:15:37: 7000000 INFO @ Wed, 22 Apr 2020 10:15:39: 19000000 INFO @ Wed, 22 Apr 2020 10:15:40: 13000000 INFO @ Wed, 22 Apr 2020 10:15:42: 8000000 INFO @ Wed, 22 Apr 2020 10:15:44: 20000000 INFO @ Wed, 22 Apr 2020 10:15:46: 14000000 INFO @ Wed, 22 Apr 2020 10:15:48: 9000000 INFO @ Wed, 22 Apr 2020 10:15:50: 21000000 INFO @ Wed, 22 Apr 2020 10:15:52: 15000000 INFO @ Wed, 22 Apr 2020 10:15:54: 10000000 INFO @ Wed, 22 Apr 2020 10:15:55: 22000000 INFO @ Wed, 22 Apr 2020 10:15:57: 16000000 INFO @ Wed, 22 Apr 2020 10:16:00: 11000000 INFO @ Wed, 22 Apr 2020 10:16:01: 23000000 INFO @ Wed, 22 Apr 2020 10:16:03: 17000000 INFO @ Wed, 22 Apr 2020 10:16:05: 12000000 INFO @ Wed, 22 Apr 2020 10:16:07: 24000000 INFO @ Wed, 22 Apr 2020 10:16:09: 18000000 INFO @ Wed, 22 Apr 2020 10:16:11: 13000000 INFO @ Wed, 22 Apr 2020 10:16:12: 25000000 INFO @ Wed, 22 Apr 2020 10:16:15: 19000000 INFO @ Wed, 22 Apr 2020 10:16:17: 14000000 INFO @ Wed, 22 Apr 2020 10:16:18: 26000000 INFO @ Wed, 22 Apr 2020 10:16:20: 20000000 INFO @ Wed, 22 Apr 2020 10:16:23: 15000000 INFO @ Wed, 22 Apr 2020 10:16:24: 27000000 INFO @ Wed, 22 Apr 2020 10:16:26: 21000000 INFO @ Wed, 22 Apr 2020 10:16:28: 16000000 INFO @ Wed, 22 Apr 2020 10:16:30: 28000000 INFO @ Wed, 22 Apr 2020 10:16:32: 22000000 INFO @ Wed, 22 Apr 2020 10:16:34: 17000000 INFO @ Wed, 22 Apr 2020 10:16:36: 29000000 INFO @ Wed, 22 Apr 2020 10:16:37: 23000000 INFO @ Wed, 22 Apr 2020 10:16:40: 18000000 INFO @ Wed, 22 Apr 2020 10:16:41: 30000000 INFO @ Wed, 22 Apr 2020 10:16:43: 24000000 INFO @ Wed, 22 Apr 2020 10:16:46: 19000000 INFO @ Wed, 22 Apr 2020 10:16:47: 31000000 INFO @ Wed, 22 Apr 2020 10:16:49: 25000000 INFO @ Wed, 22 Apr 2020 10:16:51: 20000000 INFO @ Wed, 22 Apr 2020 10:16:53: 32000000 INFO @ Wed, 22 Apr 2020 10:16:54: 26000000 INFO @ Wed, 22 Apr 2020 10:16:57: 21000000 INFO @ Wed, 22 Apr 2020 10:16:59: 33000000 INFO @ Wed, 22 Apr 2020 10:17:00: 27000000 INFO @ Wed, 22 Apr 2020 10:17:03: 22000000 INFO @ Wed, 22 Apr 2020 10:17:04: 34000000 INFO @ Wed, 22 Apr 2020 10:17:06: 28000000 INFO @ Wed, 22 Apr 2020 10:17:08: 23000000 INFO @ Wed, 22 Apr 2020 10:17:10: 35000000 INFO @ Wed, 22 Apr 2020 10:17:11: 29000000 INFO @ Wed, 22 Apr 2020 10:17:14: 24000000 INFO @ Wed, 22 Apr 2020 10:17:16: 36000000 INFO @ Wed, 22 Apr 2020 10:17:17: 30000000 INFO @ Wed, 22 Apr 2020 10:17:20: 25000000 INFO @ Wed, 22 Apr 2020 10:17:21: 37000000 INFO @ Wed, 22 Apr 2020 10:17:23: 31000000 INFO @ Wed, 22 Apr 2020 10:17:25: 26000000 INFO @ Wed, 22 Apr 2020 10:17:27: 38000000 INFO @ Wed, 22 Apr 2020 10:17:28: 32000000 INFO @ Wed, 22 Apr 2020 10:17:31: 27000000 INFO @ Wed, 22 Apr 2020 10:17:33: 39000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:17:34: 33000000 INFO @ Wed, 22 Apr 2020 10:17:37: 28000000 INFO @ Wed, 22 Apr 2020 10:17:39: 40000000 INFO @ Wed, 22 Apr 2020 10:17:40: 34000000 INFO @ Wed, 22 Apr 2020 10:17:42: 29000000 INFO @ Wed, 22 Apr 2020 10:17:44: 41000000 INFO @ Wed, 22 Apr 2020 10:17:45: 35000000 INFO @ Wed, 22 Apr 2020 10:17:48: 30000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:17:50: 42000000 INFO @ Wed, 22 Apr 2020 10:17:51: 36000000 INFO @ Wed, 22 Apr 2020 10:17:54: 31000000 INFO @ Wed, 22 Apr 2020 10:17:56: 43000000 INFO @ Wed, 22 Apr 2020 10:17:57: 37000000 INFO @ Wed, 22 Apr 2020 10:18:00: 32000000 INFO @ Wed, 22 Apr 2020 10:18:01: 44000000 INFO @ Wed, 22 Apr 2020 10:18:02: 38000000 INFO @ Wed, 22 Apr 2020 10:18:05: 33000000 INFO @ Wed, 22 Apr 2020 10:18:06: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:18:06: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:18:06: #1 total tags in treatment: 22211878 INFO @ Wed, 22 Apr 2020 10:18:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:18:06: #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 10:18:06: #1 tags after filtering in treatment: 13053512 INFO @ Wed, 22 Apr 2020 10:18:06: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 10:18:06: #1 finished! INFO @ Wed, 22 Apr 2020 10:18:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:18:07: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:18:07: 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 10:18:07: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:18:08: 39000000 INFO @ Wed, 22 Apr 2020 10:18:11: 34000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.05_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/SRX7409566/SRX7409566.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:18:14: 40000000 INFO @ Wed, 22 Apr 2020 10:18:17: 35000000 INFO @ Wed, 22 Apr 2020 10:18:19: 41000000 INFO @ Wed, 22 Apr 2020 10:18:22: 36000000 INFO @ Wed, 22 Apr 2020 10:18:25: 42000000 INFO @ Wed, 22 Apr 2020 10:18:28: 37000000 INFO @ Wed, 22 Apr 2020 10:18:31: 43000000 INFO @ Wed, 22 Apr 2020 10:18:34: 38000000 INFO @ Wed, 22 Apr 2020 10:18:36: 44000000 INFO @ Wed, 22 Apr 2020 10:18:39: 39000000 INFO @ Wed, 22 Apr 2020 10:18:41: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:18:41: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:18:41: #1 total tags in treatment: 22211878 INFO @ Wed, 22 Apr 2020 10:18:41: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:18:41: #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 10:18:41: #1 tags after filtering in treatment: 13053512 INFO @ Wed, 22 Apr 2020 10:18:41: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 10:18:41: #1 finished! INFO @ Wed, 22 Apr 2020 10:18:41: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:18:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:18:42: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:18:42: 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 10:18:42: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:18:45: 40000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.10_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/SRX7409566/SRX7409566.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:18:50: 41000000 INFO @ Wed, 22 Apr 2020 10:18:55: 42000000 INFO @ Wed, 22 Apr 2020 10:19:01: 43000000 INFO @ Wed, 22 Apr 2020 10:19:06: 44000000 INFO @ Wed, 22 Apr 2020 10:19:10: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:19:10: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:19:10: #1 total tags in treatment: 22211878 INFO @ Wed, 22 Apr 2020 10:19:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:19:10: #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 10:19:10: #1 tags after filtering in treatment: 13053512 INFO @ Wed, 22 Apr 2020 10:19:10: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 10:19:10: #1 finished! INFO @ Wed, 22 Apr 2020 10:19:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:19:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:19:11: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:19:11: 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 10:19:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.20_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/SRX7409566/SRX7409566.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409566/SRX7409566.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling