Job ID = 5791308 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:30:42 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 ) 2020-04-22T00:39:38 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 ) 2020-04-22T00:41:11 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 : 34,833,608 reads read : 69,667,216 reads written : 69,667,216 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: 00:19:44 34833608 reads; of these: 34833608 (100.00%) were paired; of these: 328329 (0.94%) aligned concordantly 0 times 29385417 (84.36%) aligned concordantly exactly 1 time 5119862 (14.70%) aligned concordantly >1 times ---- 328329 pairs aligned concordantly 0 times; of these: 79540 (24.23%) aligned discordantly 1 time ---- 248789 pairs aligned 0 times concordantly or discordantly; of these: 497578 mates make up the pairs; of these: 287362 (57.75%) aligned 0 times 144157 (28.97%) aligned exactly 1 time 66059 (13.28%) aligned >1 times 99.59% overall alignment rate Time searching: 00:19:44 Overall time: 00:19:44 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 32 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] 10750804 / 34515946 = 0.3115 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 10:19:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.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 10:19:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:19:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:19:17: 1000000 INFO @ Wed, 22 Apr 2020 10:19:24: 2000000 INFO @ Wed, 22 Apr 2020 10:19:30: 3000000 INFO @ Wed, 22 Apr 2020 10:19:36: 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 10:19:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.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 10:19:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:19:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:19:43: 5000000 INFO @ Wed, 22 Apr 2020 10:19:48: 1000000 INFO @ Wed, 22 Apr 2020 10:19:49: 6000000 INFO @ Wed, 22 Apr 2020 10:19:55: 2000000 INFO @ Wed, 22 Apr 2020 10:19:56: 7000000 INFO @ Wed, 22 Apr 2020 10:20:01: 3000000 INFO @ Wed, 22 Apr 2020 10:20:04: 8000000 INFO @ Wed, 22 Apr 2020 10:20:08: 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 10:20:11: 9000000 INFO @ Wed, 22 Apr 2020 10:20:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.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 10:20:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:20:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:20:14: 5000000 INFO @ Wed, 22 Apr 2020 10:20:18: 10000000 INFO @ Wed, 22 Apr 2020 10:20:18: 1000000 INFO @ Wed, 22 Apr 2020 10:20:21: 6000000 INFO @ Wed, 22 Apr 2020 10:20:24: 11000000 INFO @ Wed, 22 Apr 2020 10:20:25: 2000000 INFO @ Wed, 22 Apr 2020 10:20:27: 7000000 INFO @ Wed, 22 Apr 2020 10:20:30: 12000000 INFO @ Wed, 22 Apr 2020 10:20:33: 8000000 INFO @ Wed, 22 Apr 2020 10:20:33: 3000000 INFO @ Wed, 22 Apr 2020 10:20:35: 13000000 INFO @ Wed, 22 Apr 2020 10:20:40: 9000000 INFO @ Wed, 22 Apr 2020 10:20:40: 4000000 INFO @ Wed, 22 Apr 2020 10:20:41: 14000000 INFO @ Wed, 22 Apr 2020 10:20:46: 10000000 INFO @ Wed, 22 Apr 2020 10:20:46: 15000000 INFO @ Wed, 22 Apr 2020 10:20:47: 5000000 INFO @ Wed, 22 Apr 2020 10:20:52: 16000000 INFO @ Wed, 22 Apr 2020 10:20:52: 11000000 INFO @ Wed, 22 Apr 2020 10:20:54: 6000000 INFO @ Wed, 22 Apr 2020 10:20:58: 17000000 INFO @ Wed, 22 Apr 2020 10:20:59: 12000000 INFO @ Wed, 22 Apr 2020 10:21:00: 7000000 INFO @ Wed, 22 Apr 2020 10:21:03: 18000000 INFO @ Wed, 22 Apr 2020 10:21:05: 13000000 INFO @ Wed, 22 Apr 2020 10:21:07: 8000000 INFO @ Wed, 22 Apr 2020 10:21:09: 19000000 INFO @ Wed, 22 Apr 2020 10:21:11: 14000000 INFO @ Wed, 22 Apr 2020 10:21:14: 9000000 INFO @ Wed, 22 Apr 2020 10:21:15: 20000000 INFO @ Wed, 22 Apr 2020 10:21:18: 15000000 INFO @ Wed, 22 Apr 2020 10:21:20: 21000000 INFO @ Wed, 22 Apr 2020 10:21:20: 10000000 INFO @ Wed, 22 Apr 2020 10:21:24: 16000000 INFO @ Wed, 22 Apr 2020 10:21:26: 22000000 INFO @ Wed, 22 Apr 2020 10:21:27: 11000000 INFO @ Wed, 22 Apr 2020 10:21:30: 17000000 INFO @ Wed, 22 Apr 2020 10:21:31: 23000000 INFO @ Wed, 22 Apr 2020 10:21:33: 12000000 INFO @ Wed, 22 Apr 2020 10:21:37: 18000000 INFO @ Wed, 22 Apr 2020 10:21:37: 24000000 INFO @ Wed, 22 Apr 2020 10:21:40: 13000000 INFO @ Wed, 22 Apr 2020 10:21:43: 25000000 INFO @ Wed, 22 Apr 2020 10:21:43: 19000000 INFO @ Wed, 22 Apr 2020 10:21:46: 14000000 INFO @ Wed, 22 Apr 2020 10:21:48: 26000000 INFO @ Wed, 22 Apr 2020 10:21:50: 20000000 INFO @ Wed, 22 Apr 2020 10:21:52: 15000000 INFO @ Wed, 22 Apr 2020 10:21:54: 27000000 INFO @ Wed, 22 Apr 2020 10:21:56: 21000000 INFO @ Wed, 22 Apr 2020 10:21:59: 16000000 INFO @ Wed, 22 Apr 2020 10:21:59: 28000000 INFO @ Wed, 22 Apr 2020 10:22:02: 22000000 INFO @ Wed, 22 Apr 2020 10:22:05: 29000000 INFO @ Wed, 22 Apr 2020 10:22:05: 17000000 INFO @ Wed, 22 Apr 2020 10:22:09: 23000000 INFO @ Wed, 22 Apr 2020 10:22:11: 30000000 INFO @ Wed, 22 Apr 2020 10:22:12: 18000000 INFO @ Wed, 22 Apr 2020 10:22:15: 24000000 INFO @ Wed, 22 Apr 2020 10:22:16: 31000000 INFO @ Wed, 22 Apr 2020 10:22:18: 19000000 INFO @ Wed, 22 Apr 2020 10:22:21: 25000000 INFO @ Wed, 22 Apr 2020 10:22:22: 32000000 INFO @ Wed, 22 Apr 2020 10:22:25: 20000000 INFO @ Wed, 22 Apr 2020 10:22:27: 33000000 INFO @ Wed, 22 Apr 2020 10:22:27: 26000000 INFO @ Wed, 22 Apr 2020 10:22:31: 21000000 INFO @ Wed, 22 Apr 2020 10:22:33: 34000000 INFO @ Wed, 22 Apr 2020 10:22:34: 27000000 INFO @ Wed, 22 Apr 2020 10:22:38: 22000000 INFO @ Wed, 22 Apr 2020 10:22:38: 35000000 INFO @ Wed, 22 Apr 2020 10:22:40: 28000000 INFO @ Wed, 22 Apr 2020 10:22:44: 23000000 INFO @ Wed, 22 Apr 2020 10:22:44: 36000000 INFO @ Wed, 22 Apr 2020 10:22:47: 29000000 INFO @ Wed, 22 Apr 2020 10:22:50: 37000000 INFO @ Wed, 22 Apr 2020 10:22:50: 24000000 INFO @ Wed, 22 Apr 2020 10:22:53: 30000000 INFO @ Wed, 22 Apr 2020 10:22:55: 38000000 INFO @ Wed, 22 Apr 2020 10:22:57: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:22:59: 31000000 INFO @ Wed, 22 Apr 2020 10:23:01: 39000000 INFO @ Wed, 22 Apr 2020 10:23:03: 26000000 INFO @ Wed, 22 Apr 2020 10:23:06: 32000000 INFO @ Wed, 22 Apr 2020 10:23:06: 40000000 INFO @ Wed, 22 Apr 2020 10:23:10: 27000000 INFO @ Wed, 22 Apr 2020 10:23:12: 33000000 INFO @ Wed, 22 Apr 2020 10:23:12: 41000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:23:16: 28000000 INFO @ Wed, 22 Apr 2020 10:23:17: 42000000 INFO @ Wed, 22 Apr 2020 10:23:18: 34000000 INFO @ Wed, 22 Apr 2020 10:23:22: 29000000 INFO @ Wed, 22 Apr 2020 10:23:23: 43000000 INFO @ Wed, 22 Apr 2020 10:23:24: 35000000 INFO @ Wed, 22 Apr 2020 10:23:28: 30000000 INFO @ Wed, 22 Apr 2020 10:23:29: 44000000 INFO @ Wed, 22 Apr 2020 10:23:31: 36000000 INFO @ Wed, 22 Apr 2020 10:23:34: 45000000 INFO @ Wed, 22 Apr 2020 10:23:35: 31000000 INFO @ Wed, 22 Apr 2020 10:23:37: 37000000 INFO @ Wed, 22 Apr 2020 10:23:40: 46000000 INFO @ Wed, 22 Apr 2020 10:23:41: 32000000 INFO @ Wed, 22 Apr 2020 10:23:43: 38000000 INFO @ Wed, 22 Apr 2020 10:23:45: 47000000 INFO @ Wed, 22 Apr 2020 10:23:47: 33000000 INFO @ Wed, 22 Apr 2020 10:23:49: 39000000 INFO @ Wed, 22 Apr 2020 10:23:50: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:23:50: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:23:50: #1 total tags in treatment: 23756876 INFO @ Wed, 22 Apr 2020 10:23:50: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:23:50: #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 10:23:51: #1 tags after filtering in treatment: 13609944 INFO @ Wed, 22 Apr 2020 10:23:51: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 10:23:51: #1 finished! INFO @ Wed, 22 Apr 2020 10:23:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:23:52: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:23:52: 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 10:23:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:23:53: 34000000 INFO @ Wed, 22 Apr 2020 10:23:55: 40000000 INFO @ Wed, 22 Apr 2020 10:24:00: 35000000 INFO @ Wed, 22 Apr 2020 10:24:02: 41000000 INFO @ Wed, 22 Apr 2020 10:24:06: 36000000 INFO @ Wed, 22 Apr 2020 10:24:08: 42000000 INFO @ Wed, 22 Apr 2020 10:24:12: 37000000 INFO @ Wed, 22 Apr 2020 10:24:14: 43000000 INFO @ Wed, 22 Apr 2020 10:24:18: 38000000 INFO @ Wed, 22 Apr 2020 10:24:20: 44000000 INFO @ Wed, 22 Apr 2020 10:24:24: 39000000 INFO @ Wed, 22 Apr 2020 10:24:26: 45000000 INFO @ Wed, 22 Apr 2020 10:24:30: 40000000 INFO @ Wed, 22 Apr 2020 10:24:32: 46000000 INFO @ Wed, 22 Apr 2020 10:24:36: 41000000 INFO @ Wed, 22 Apr 2020 10:24:38: 47000000 INFO @ Wed, 22 Apr 2020 10:24:42: 42000000 INFO @ Wed, 22 Apr 2020 10:24:44: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:24:44: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:24:44: #1 total tags in treatment: 23756876 INFO @ Wed, 22 Apr 2020 10:24:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:24:44: #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 10:24:44: #1 tags after filtering in treatment: 13609944 INFO @ Wed, 22 Apr 2020 10:24:44: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 10:24:44: #1 finished! INFO @ Wed, 22 Apr 2020 10:24:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:24:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:24:45: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:24:45: 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 10:24:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.10_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/SRX7409564/SRX7409564.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:24:48: 43000000 INFO @ Wed, 22 Apr 2020 10:24:54: 44000000 INFO @ Wed, 22 Apr 2020 10:25:00: 45000000 INFO @ Wed, 22 Apr 2020 10:25:06: 46000000 INFO @ Wed, 22 Apr 2020 10:25:11: 47000000 INFO @ Wed, 22 Apr 2020 10:25:17: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:25:17: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:25:17: #1 total tags in treatment: 23756876 INFO @ Wed, 22 Apr 2020 10:25:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:25:17: #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 10:25:17: #1 tags after filtering in treatment: 13609944 INFO @ Wed, 22 Apr 2020 10:25:17: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 10:25:17: #1 finished! INFO @ Wed, 22 Apr 2020 10:25:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:25:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:25:18: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:25:18: 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 10:25:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.20_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/SRX7409564/SRX7409564.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409564/SRX7409564.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling