Job ID = 5791672 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:22:01 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 : 31,952,831 reads read : 63,905,662 reads written : 63,905,662 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: 00:20:25 31952831 reads; of these: 31952831 (100.00%) were paired; of these: 2969985 (9.29%) aligned concordantly 0 times 24668766 (77.20%) aligned concordantly exactly 1 time 4314080 (13.50%) aligned concordantly >1 times ---- 2969985 pairs aligned concordantly 0 times; of these: 17626 (0.59%) aligned discordantly 1 time ---- 2952359 pairs aligned 0 times concordantly or discordantly; of these: 5904718 mates make up the pairs; of these: 5303288 (89.81%) aligned 0 times 487285 (8.25%) aligned exactly 1 time 114145 (1.93%) aligned >1 times 91.70% overall alignment rate Time searching: 00:20:25 Overall time: 00:20:25 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] 10406799 / 28989187 = 0.3590 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 11:13:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.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 11:13:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:13:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:13:23: 1000000 INFO @ Wed, 22 Apr 2020 11:13:28: 2000000 INFO @ Wed, 22 Apr 2020 11:13:33: 3000000 INFO @ Wed, 22 Apr 2020 11:13:38: 4000000 INFO @ Wed, 22 Apr 2020 11:13:42: 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 11:13:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.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 11:13:47: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:13:47: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:13:47: 6000000 INFO @ Wed, 22 Apr 2020 11:13:53: 7000000 INFO @ Wed, 22 Apr 2020 11:13:53: 1000000 INFO @ Wed, 22 Apr 2020 11:13:58: 8000000 INFO @ Wed, 22 Apr 2020 11:13:58: 2000000 INFO @ Wed, 22 Apr 2020 11:14:04: 9000000 INFO @ Wed, 22 Apr 2020 11:14:04: 3000000 INFO @ Wed, 22 Apr 2020 11:14:09: 10000000 INFO @ Wed, 22 Apr 2020 11:14:11: 4000000 INFO @ Wed, 22 Apr 2020 11:14:14: 11000000 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 11:14:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.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 11:14:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:14:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:14:17: 5000000 INFO @ Wed, 22 Apr 2020 11:14:19: 12000000 INFO @ Wed, 22 Apr 2020 11:14:22: 1000000 INFO @ Wed, 22 Apr 2020 11:14:23: 6000000 INFO @ Wed, 22 Apr 2020 11:14:25: 13000000 INFO @ Wed, 22 Apr 2020 11:14:28: 2000000 INFO @ Wed, 22 Apr 2020 11:14:29: 7000000 INFO @ Wed, 22 Apr 2020 11:14:30: 14000000 INFO @ Wed, 22 Apr 2020 11:14:34: 3000000 INFO @ Wed, 22 Apr 2020 11:14:35: 15000000 INFO @ Wed, 22 Apr 2020 11:14:35: 8000000 INFO @ Wed, 22 Apr 2020 11:14:39: 4000000 INFO @ Wed, 22 Apr 2020 11:14:40: 16000000 INFO @ Wed, 22 Apr 2020 11:14:42: 9000000 INFO @ Wed, 22 Apr 2020 11:14:45: 5000000 INFO @ Wed, 22 Apr 2020 11:14:46: 17000000 INFO @ Wed, 22 Apr 2020 11:14:48: 10000000 INFO @ Wed, 22 Apr 2020 11:14:51: 6000000 INFO @ Wed, 22 Apr 2020 11:14:52: 18000000 INFO @ Wed, 22 Apr 2020 11:14:54: 11000000 INFO @ Wed, 22 Apr 2020 11:14:56: 7000000 INFO @ Wed, 22 Apr 2020 11:14:57: 19000000 INFO @ Wed, 22 Apr 2020 11:15:00: 12000000 INFO @ Wed, 22 Apr 2020 11:15:02: 8000000 INFO @ Wed, 22 Apr 2020 11:15:03: 20000000 INFO @ Wed, 22 Apr 2020 11:15:06: 13000000 INFO @ Wed, 22 Apr 2020 11:15:08: 9000000 INFO @ Wed, 22 Apr 2020 11:15:08: 21000000 INFO @ Wed, 22 Apr 2020 11:15:12: 14000000 INFO @ Wed, 22 Apr 2020 11:15:13: 10000000 INFO @ Wed, 22 Apr 2020 11:15:13: 22000000 INFO @ Wed, 22 Apr 2020 11:15:18: 15000000 INFO @ Wed, 22 Apr 2020 11:15:18: 11000000 INFO @ Wed, 22 Apr 2020 11:15:19: 23000000 INFO @ Wed, 22 Apr 2020 11:15:24: 16000000 INFO @ Wed, 22 Apr 2020 11:15:24: 24000000 INFO @ Wed, 22 Apr 2020 11:15:25: 12000000 INFO @ Wed, 22 Apr 2020 11:15:30: 25000000 INFO @ Wed, 22 Apr 2020 11:15:30: 17000000 INFO @ Wed, 22 Apr 2020 11:15:31: 13000000 INFO @ Wed, 22 Apr 2020 11:15:35: 26000000 INFO @ Wed, 22 Apr 2020 11:15:36: 18000000 INFO @ Wed, 22 Apr 2020 11:15:36: 14000000 INFO @ Wed, 22 Apr 2020 11:15:40: 27000000 INFO @ Wed, 22 Apr 2020 11:15:42: 19000000 INFO @ Wed, 22 Apr 2020 11:15:42: 15000000 INFO @ Wed, 22 Apr 2020 11:15:46: 28000000 INFO @ Wed, 22 Apr 2020 11:15:48: 16000000 INFO @ Wed, 22 Apr 2020 11:15:48: 20000000 INFO @ Wed, 22 Apr 2020 11:15:52: 29000000 INFO @ Wed, 22 Apr 2020 11:15:54: 17000000 INFO @ Wed, 22 Apr 2020 11:15:55: 21000000 INFO @ Wed, 22 Apr 2020 11:15:57: 30000000 INFO @ Wed, 22 Apr 2020 11:15:59: 18000000 INFO @ Wed, 22 Apr 2020 11:16:01: 22000000 INFO @ Wed, 22 Apr 2020 11:16:03: 31000000 INFO @ Wed, 22 Apr 2020 11:16:04: 19000000 INFO @ Wed, 22 Apr 2020 11:16:07: 23000000 INFO @ Wed, 22 Apr 2020 11:16:08: 32000000 INFO @ Wed, 22 Apr 2020 11:16:10: 20000000 INFO @ Wed, 22 Apr 2020 11:16:13: 24000000 INFO @ Wed, 22 Apr 2020 11:16:13: 33000000 INFO @ Wed, 22 Apr 2020 11:16:15: 21000000 INFO @ Wed, 22 Apr 2020 11:16:19: 34000000 INFO @ Wed, 22 Apr 2020 11:16:19: 25000000 INFO @ Wed, 22 Apr 2020 11:16:21: 22000000 INFO @ Wed, 22 Apr 2020 11:16:24: 35000000 INFO @ Wed, 22 Apr 2020 11:16:26: 26000000 INFO @ Wed, 22 Apr 2020 11:16:27: 23000000 INFO @ Wed, 22 Apr 2020 11:16:29: 36000000 INFO @ Wed, 22 Apr 2020 11:16:32: 27000000 INFO @ Wed, 22 Apr 2020 11:16:32: 24000000 INFO @ Wed, 22 Apr 2020 11:16:35: 37000000 INFO @ Wed, 22 Apr 2020 11:16:37: 25000000 INFO @ Wed, 22 Apr 2020 11:16:38: 28000000 INFO @ Wed, 22 Apr 2020 11:16:39: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:16:39: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:16:39: #1 total tags in treatment: 18578126 INFO @ Wed, 22 Apr 2020 11:16:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:16:39: #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 11:16:39: #1 tags after filtering in treatment: 10507572 INFO @ Wed, 22 Apr 2020 11:16:39: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 11:16:39: #1 finished! INFO @ Wed, 22 Apr 2020 11:16:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:16:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:16:40: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:16:40: 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 11:16:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.05_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/SRX7409633/SRX7409633.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:16:44: 26000000 INFO @ Wed, 22 Apr 2020 11:16:44: 29000000 INFO @ Wed, 22 Apr 2020 11:16:50: 27000000 INFO @ Wed, 22 Apr 2020 11:16:50: 30000000 INFO @ Wed, 22 Apr 2020 11:16:56: 31000000 INFO @ Wed, 22 Apr 2020 11:16:57: 28000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:17:02: 32000000 INFO @ Wed, 22 Apr 2020 11:17:05: 29000000 INFO @ Wed, 22 Apr 2020 11:17:08: 33000000 INFO @ Wed, 22 Apr 2020 11:17:12: 30000000 INFO @ Wed, 22 Apr 2020 11:17:14: 34000000 INFO @ Wed, 22 Apr 2020 11:17:17: 31000000 INFO @ Wed, 22 Apr 2020 11:17:19: 35000000 INFO @ Wed, 22 Apr 2020 11:17:23: 32000000 INFO @ Wed, 22 Apr 2020 11:17:24: 36000000 INFO @ Wed, 22 Apr 2020 11:17:29: 33000000 INFO @ Wed, 22 Apr 2020 11:17:29: 37000000 INFO @ Wed, 22 Apr 2020 11:17:34: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:17:34: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:17:34: #1 total tags in treatment: 18578126 INFO @ Wed, 22 Apr 2020 11:17:34: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:17:34: #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 11:17:35: 34000000 INFO @ Wed, 22 Apr 2020 11:17:35: #1 tags after filtering in treatment: 10507572 INFO @ Wed, 22 Apr 2020 11:17:35: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 11:17:35: #1 finished! INFO @ Wed, 22 Apr 2020 11:17:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:17:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:17:35: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:17:35: 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 11:17:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.10_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/SRX7409633/SRX7409633.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:17:40: 35000000 INFO @ Wed, 22 Apr 2020 11:17:46: 36000000 INFO @ Wed, 22 Apr 2020 11:17:51: 37000000 INFO @ Wed, 22 Apr 2020 11:17:55: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:17:55: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:17:55: #1 total tags in treatment: 18578126 INFO @ Wed, 22 Apr 2020 11:17:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:17:55: #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 11:17:55: #1 tags after filtering in treatment: 10507572 INFO @ Wed, 22 Apr 2020 11:17:55: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 11:17:55: #1 finished! INFO @ Wed, 22 Apr 2020 11:17:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:17:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:17:56: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:17:56: 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 11:17:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.20_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/SRX7409633/SRX7409633.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409633/SRX7409633.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling