Job ID = 5791671 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:19:28 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 ) 2020-04-22T01:20:14 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 ) 2020-04-22T01:24:53 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 ) 2020-04-22T01:24:53 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 : 32,448,837 reads read : 64,897,674 reads written : 64,897,674 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: 00:21:57 32448837 reads; of these: 32448837 (100.00%) were paired; of these: 2524362 (7.78%) aligned concordantly 0 times 25528645 (78.67%) aligned concordantly exactly 1 time 4395830 (13.55%) aligned concordantly >1 times ---- 2524362 pairs aligned concordantly 0 times; of these: 22976 (0.91%) aligned discordantly 1 time ---- 2501386 pairs aligned 0 times concordantly or discordantly; of these: 5002772 mates make up the pairs; of these: 4462512 (89.20%) aligned 0 times 425749 (8.51%) aligned exactly 1 time 114511 (2.29%) aligned >1 times 93.12% overall alignment rate Time searching: 00:21:57 Overall time: 00:21:57 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] 10036286 / 29934696 = 0.3353 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 11:13:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.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 11:13:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:13:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:13:25: 1000000 INFO @ Wed, 22 Apr 2020 11:13:30: 2000000 INFO @ Wed, 22 Apr 2020 11:13:35: 3000000 INFO @ Wed, 22 Apr 2020 11:13:40: 4000000 INFO @ Wed, 22 Apr 2020 11:13:45: 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 11:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.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 11:13:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:13:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:13:51: 6000000 INFO @ Wed, 22 Apr 2020 11:13:56: 1000000 INFO @ Wed, 22 Apr 2020 11:13:57: 7000000 INFO @ Wed, 22 Apr 2020 11:14:03: 8000000 INFO @ Wed, 22 Apr 2020 11:14:03: 2000000 INFO @ Wed, 22 Apr 2020 11:14:09: 9000000 INFO @ Wed, 22 Apr 2020 11:14:10: 3000000 INFO @ Wed, 22 Apr 2020 11:14:15: 10000000 INFO @ Wed, 22 Apr 2020 11:14:17: 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 11:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.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 11:14:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:14:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:14:20: 11000000 INFO @ Wed, 22 Apr 2020 11:14:23: 5000000 INFO @ Wed, 22 Apr 2020 11:14:26: 1000000 INFO @ Wed, 22 Apr 2020 11:14:26: 12000000 INFO @ Wed, 22 Apr 2020 11:14:30: 6000000 INFO @ Wed, 22 Apr 2020 11:14:32: 2000000 INFO @ Wed, 22 Apr 2020 11:14:32: 13000000 INFO @ Wed, 22 Apr 2020 11:14:37: 7000000 INFO @ Wed, 22 Apr 2020 11:14:38: 3000000 INFO @ Wed, 22 Apr 2020 11:14:38: 14000000 INFO @ Wed, 22 Apr 2020 11:14:44: 8000000 INFO @ Wed, 22 Apr 2020 11:14:44: 4000000 INFO @ Wed, 22 Apr 2020 11:14:44: 15000000 INFO @ Wed, 22 Apr 2020 11:14:50: 5000000 INFO @ Wed, 22 Apr 2020 11:14:50: 16000000 INFO @ Wed, 22 Apr 2020 11:14:50: 9000000 INFO @ Wed, 22 Apr 2020 11:14:56: 6000000 INFO @ Wed, 22 Apr 2020 11:14:56: 17000000 INFO @ Wed, 22 Apr 2020 11:14:57: 10000000 INFO @ Wed, 22 Apr 2020 11:15:02: 7000000 INFO @ Wed, 22 Apr 2020 11:15:02: 18000000 INFO @ Wed, 22 Apr 2020 11:15:03: 11000000 INFO @ Wed, 22 Apr 2020 11:15:07: 8000000 INFO @ Wed, 22 Apr 2020 11:15:08: 19000000 INFO @ Wed, 22 Apr 2020 11:15:09: 12000000 INFO @ Wed, 22 Apr 2020 11:15:13: 9000000 INFO @ Wed, 22 Apr 2020 11:15:14: 20000000 INFO @ Wed, 22 Apr 2020 11:15:16: 13000000 INFO @ Wed, 22 Apr 2020 11:15:19: 10000000 INFO @ Wed, 22 Apr 2020 11:15:20: 21000000 INFO @ Wed, 22 Apr 2020 11:15:23: 14000000 INFO @ Wed, 22 Apr 2020 11:15:25: 11000000 INFO @ Wed, 22 Apr 2020 11:15:26: 22000000 INFO @ Wed, 22 Apr 2020 11:15:30: 15000000 INFO @ Wed, 22 Apr 2020 11:15:31: 12000000 INFO @ Wed, 22 Apr 2020 11:15:32: 23000000 INFO @ Wed, 22 Apr 2020 11:15:36: 16000000 INFO @ Wed, 22 Apr 2020 11:15:37: 13000000 INFO @ Wed, 22 Apr 2020 11:15:38: 24000000 INFO @ Wed, 22 Apr 2020 11:15:43: 17000000 INFO @ Wed, 22 Apr 2020 11:15:43: 14000000 INFO @ Wed, 22 Apr 2020 11:15:44: 25000000 INFO @ Wed, 22 Apr 2020 11:15:49: 15000000 INFO @ Wed, 22 Apr 2020 11:15:49: 26000000 INFO @ Wed, 22 Apr 2020 11:15:49: 18000000 INFO @ Wed, 22 Apr 2020 11:15:55: 16000000 INFO @ Wed, 22 Apr 2020 11:15:55: 27000000 INFO @ Wed, 22 Apr 2020 11:15:56: 19000000 INFO @ Wed, 22 Apr 2020 11:16:01: 17000000 INFO @ Wed, 22 Apr 2020 11:16:01: 28000000 INFO @ Wed, 22 Apr 2020 11:16:03: 20000000 INFO @ Wed, 22 Apr 2020 11:16:07: 18000000 INFO @ Wed, 22 Apr 2020 11:16:07: 29000000 INFO @ Wed, 22 Apr 2020 11:16:09: 21000000 INFO @ Wed, 22 Apr 2020 11:16:13: 30000000 INFO @ Wed, 22 Apr 2020 11:16:13: 19000000 INFO @ Wed, 22 Apr 2020 11:16:16: 22000000 INFO @ Wed, 22 Apr 2020 11:16:19: 31000000 INFO @ Wed, 22 Apr 2020 11:16:19: 20000000 INFO @ Wed, 22 Apr 2020 11:16:23: 23000000 INFO @ Wed, 22 Apr 2020 11:16:24: 32000000 INFO @ Wed, 22 Apr 2020 11:16:25: 21000000 INFO @ Wed, 22 Apr 2020 11:16:29: 24000000 INFO @ Wed, 22 Apr 2020 11:16:30: 33000000 INFO @ Wed, 22 Apr 2020 11:16:31: 22000000 INFO @ Wed, 22 Apr 2020 11:16:36: 25000000 INFO @ Wed, 22 Apr 2020 11:16:36: 34000000 INFO @ Wed, 22 Apr 2020 11:16:37: 23000000 INFO @ Wed, 22 Apr 2020 11:16:42: 35000000 INFO @ Wed, 22 Apr 2020 11:16:42: 26000000 INFO @ Wed, 22 Apr 2020 11:16:43: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:16:48: 36000000 INFO @ Wed, 22 Apr 2020 11:16:49: 27000000 INFO @ Wed, 22 Apr 2020 11:16:49: 25000000 INFO @ Wed, 22 Apr 2020 11:16:54: 37000000 INFO @ Wed, 22 Apr 2020 11:16:55: 26000000 INFO @ Wed, 22 Apr 2020 11:16:55: 28000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:17:00: 38000000 INFO @ Wed, 22 Apr 2020 11:17:01: 27000000 INFO @ Wed, 22 Apr 2020 11:17:02: 29000000 INFO @ Wed, 22 Apr 2020 11:17:06: 39000000 INFO @ Wed, 22 Apr 2020 11:17:07: 28000000 INFO @ Wed, 22 Apr 2020 11:17:08: 30000000 INFO @ Wed, 22 Apr 2020 11:17:11: 40000000 INFO @ Wed, 22 Apr 2020 11:17:12: 29000000 INFO @ Wed, 22 Apr 2020 11:17:14: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:17:14: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:17:14: #1 total tags in treatment: 19890626 INFO @ Wed, 22 Apr 2020 11:17:14: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:17:14: #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 11:17:14: #1 tags after filtering in treatment: 10969675 INFO @ Wed, 22 Apr 2020 11:17:14: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Apr 2020 11:17:14: #1 finished! INFO @ Wed, 22 Apr 2020 11:17:14: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:17:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:17:15: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:17:15: 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 11:17:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.05_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/SRX7409632/SRX7409632.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:17:15: 31000000 INFO @ Wed, 22 Apr 2020 11:17:18: 30000000 INFO @ Wed, 22 Apr 2020 11:17:22: 32000000 INFO @ Wed, 22 Apr 2020 11:17:24: 31000000 INFO @ Wed, 22 Apr 2020 11:17:28: 33000000 INFO @ Wed, 22 Apr 2020 11:17:30: 32000000 INFO @ Wed, 22 Apr 2020 11:17:35: 34000000 INFO @ Wed, 22 Apr 2020 11:17:36: 33000000 INFO @ Wed, 22 Apr 2020 11:17:41: 35000000 INFO @ Wed, 22 Apr 2020 11:17:42: 34000000 INFO @ Wed, 22 Apr 2020 11:17:47: 35000000 INFO @ Wed, 22 Apr 2020 11:17:48: 36000000 INFO @ Wed, 22 Apr 2020 11:17:53: 36000000 INFO @ Wed, 22 Apr 2020 11:17:54: 37000000 INFO @ Wed, 22 Apr 2020 11:17:59: 37000000 INFO @ Wed, 22 Apr 2020 11:18:01: 38000000 INFO @ Wed, 22 Apr 2020 11:18:05: 38000000 INFO @ Wed, 22 Apr 2020 11:18:07: 39000000 INFO @ Wed, 22 Apr 2020 11:18:11: 39000000 INFO @ Wed, 22 Apr 2020 11:18:14: 40000000 INFO @ Wed, 22 Apr 2020 11:18:16: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:18:16: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:18:16: #1 total tags in treatment: 19890626 INFO @ Wed, 22 Apr 2020 11:18:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:18:16: #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 11:18:17: #1 tags after filtering in treatment: 10969675 INFO @ Wed, 22 Apr 2020 11:18:17: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Apr 2020 11:18:17: #1 finished! INFO @ Wed, 22 Apr 2020 11:18:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:18:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:18:17: 40000000 INFO @ Wed, 22 Apr 2020 11:18:17: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:18:17: 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 11:18:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.10_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/SRX7409632/SRX7409632.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:18:19: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:18:19: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:18:19: #1 total tags in treatment: 19890626 INFO @ Wed, 22 Apr 2020 11:18:19: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:18:19: #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 11:18:19: #1 tags after filtering in treatment: 10969675 INFO @ Wed, 22 Apr 2020 11:18:19: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Apr 2020 11:18:19: #1 finished! INFO @ Wed, 22 Apr 2020 11:18:19: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:18:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:18:20: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:18:20: 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 11:18:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.20_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/SRX7409632/SRX7409632.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409632/SRX7409632.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling