Job ID = 5791309 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 ) 2020-04-22T00:37:11 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 ) 2020-04-22T00:37:11 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 ) 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 : 31,607,866 reads read : 63,215,732 reads written : 63,215,732 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: 00:16:29 31607866 reads; of these: 31607866 (100.00%) were paired; of these: 309883 (0.98%) aligned concordantly 0 times 26821074 (84.86%) aligned concordantly exactly 1 time 4476909 (14.16%) aligned concordantly >1 times ---- 309883 pairs aligned concordantly 0 times; of these: 64352 (20.77%) aligned discordantly 1 time ---- 245531 pairs aligned 0 times concordantly or discordantly; of these: 491062 mates make up the pairs; of these: 295732 (60.22%) aligned 0 times 137147 (27.93%) aligned exactly 1 time 58183 (11.85%) aligned >1 times 99.53% overall alignment rate Time searching: 00:16:29 Overall time: 00:16:29 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] 8952824 / 31314921 = 0.2859 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 10:12:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.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 10:12:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:12:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:12:28: 1000000 INFO @ Wed, 22 Apr 2020 10:12:33: 2000000 INFO @ Wed, 22 Apr 2020 10:12:37: 3000000 INFO @ Wed, 22 Apr 2020 10:12:42: 4000000 INFO @ Wed, 22 Apr 2020 10:12:46: 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 10:12:51: 6000000 INFO @ Wed, 22 Apr 2020 10:12:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.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 10:12:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:12:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:12:55: 7000000 INFO @ Wed, 22 Apr 2020 10:12:57: 1000000 INFO @ Wed, 22 Apr 2020 10:13:00: 8000000 INFO @ Wed, 22 Apr 2020 10:13:02: 2000000 INFO @ Wed, 22 Apr 2020 10:13:04: 9000000 INFO @ Wed, 22 Apr 2020 10:13:07: 3000000 INFO @ Wed, 22 Apr 2020 10:13:09: 10000000 INFO @ Wed, 22 Apr 2020 10:13:11: 4000000 INFO @ Wed, 22 Apr 2020 10:13:14: 11000000 INFO @ Wed, 22 Apr 2020 10:13:16: 5000000 INFO @ Wed, 22 Apr 2020 10:13:19: 12000000 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 10:13:21: 6000000 INFO @ Wed, 22 Apr 2020 10:13:23: 13000000 INFO @ Wed, 22 Apr 2020 10:13:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.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 10:13:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:13:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:13:25: 7000000 INFO @ Wed, 22 Apr 2020 10:13:28: 14000000 INFO @ Wed, 22 Apr 2020 10:13:28: 1000000 INFO @ Wed, 22 Apr 2020 10:13:30: 8000000 INFO @ Wed, 22 Apr 2020 10:13:33: 15000000 INFO @ Wed, 22 Apr 2020 10:13:33: 2000000 INFO @ Wed, 22 Apr 2020 10:13:35: 9000000 INFO @ Wed, 22 Apr 2020 10:13:37: 16000000 INFO @ Wed, 22 Apr 2020 10:13:38: 3000000 INFO @ Wed, 22 Apr 2020 10:13:39: 10000000 INFO @ Wed, 22 Apr 2020 10:13:42: 17000000 INFO @ Wed, 22 Apr 2020 10:13:42: 4000000 INFO @ Wed, 22 Apr 2020 10:13:44: 11000000 INFO @ Wed, 22 Apr 2020 10:13:47: 18000000 INFO @ Wed, 22 Apr 2020 10:13:47: 5000000 INFO @ Wed, 22 Apr 2020 10:13:48: 12000000 INFO @ Wed, 22 Apr 2020 10:13:51: 19000000 INFO @ Wed, 22 Apr 2020 10:13:51: 6000000 INFO @ Wed, 22 Apr 2020 10:13:53: 13000000 INFO @ Wed, 22 Apr 2020 10:13:56: 20000000 INFO @ Wed, 22 Apr 2020 10:13:56: 7000000 INFO @ Wed, 22 Apr 2020 10:13:58: 14000000 INFO @ Wed, 22 Apr 2020 10:14:01: 21000000 INFO @ Wed, 22 Apr 2020 10:14:01: 8000000 INFO @ Wed, 22 Apr 2020 10:14:02: 15000000 INFO @ Wed, 22 Apr 2020 10:14:05: 22000000 INFO @ Wed, 22 Apr 2020 10:14:05: 9000000 INFO @ Wed, 22 Apr 2020 10:14:07: 16000000 INFO @ Wed, 22 Apr 2020 10:14:10: 23000000 INFO @ Wed, 22 Apr 2020 10:14:10: 10000000 INFO @ Wed, 22 Apr 2020 10:14:12: 17000000 INFO @ Wed, 22 Apr 2020 10:14:14: 24000000 INFO @ Wed, 22 Apr 2020 10:14:15: 11000000 INFO @ Wed, 22 Apr 2020 10:14:16: 18000000 INFO @ Wed, 22 Apr 2020 10:14:19: 25000000 INFO @ Wed, 22 Apr 2020 10:14:19: 12000000 INFO @ Wed, 22 Apr 2020 10:14:21: 19000000 INFO @ Wed, 22 Apr 2020 10:14:23: 26000000 INFO @ Wed, 22 Apr 2020 10:14:24: 13000000 INFO @ Wed, 22 Apr 2020 10:14:25: 20000000 INFO @ Wed, 22 Apr 2020 10:14:28: 27000000 INFO @ Wed, 22 Apr 2020 10:14:29: 14000000 INFO @ Wed, 22 Apr 2020 10:14:30: 21000000 INFO @ Wed, 22 Apr 2020 10:14:32: 28000000 INFO @ Wed, 22 Apr 2020 10:14:33: 15000000 INFO @ Wed, 22 Apr 2020 10:14:35: 22000000 INFO @ Wed, 22 Apr 2020 10:14:37: 29000000 INFO @ Wed, 22 Apr 2020 10:14:38: 16000000 INFO @ Wed, 22 Apr 2020 10:14:39: 23000000 INFO @ Wed, 22 Apr 2020 10:14:41: 30000000 INFO @ Wed, 22 Apr 2020 10:14:42: 17000000 INFO @ Wed, 22 Apr 2020 10:14:44: 24000000 INFO @ Wed, 22 Apr 2020 10:14:46: 31000000 INFO @ Wed, 22 Apr 2020 10:14:47: 18000000 INFO @ Wed, 22 Apr 2020 10:14:48: 25000000 INFO @ Wed, 22 Apr 2020 10:14:50: 32000000 INFO @ Wed, 22 Apr 2020 10:14:52: 19000000 INFO @ Wed, 22 Apr 2020 10:14:53: 26000000 INFO @ Wed, 22 Apr 2020 10:14:55: 33000000 INFO @ Wed, 22 Apr 2020 10:14:56: 20000000 INFO @ Wed, 22 Apr 2020 10:14:57: 27000000 INFO @ Wed, 22 Apr 2020 10:14:59: 34000000 INFO @ Wed, 22 Apr 2020 10:15:01: 21000000 INFO @ Wed, 22 Apr 2020 10:15:02: 28000000 INFO @ Wed, 22 Apr 2020 10:15:04: 35000000 INFO @ Wed, 22 Apr 2020 10:15:05: 22000000 INFO @ Wed, 22 Apr 2020 10:15:07: 29000000 INFO @ Wed, 22 Apr 2020 10:15:08: 36000000 INFO @ Wed, 22 Apr 2020 10:15:10: 23000000 INFO @ Wed, 22 Apr 2020 10:15:11: 30000000 INFO @ Wed, 22 Apr 2020 10:15:13: 37000000 INFO @ Wed, 22 Apr 2020 10:15:14: 24000000 INFO @ Wed, 22 Apr 2020 10:15:16: 31000000 INFO @ Wed, 22 Apr 2020 10:15:17: 38000000 INFO @ Wed, 22 Apr 2020 10:15:19: 25000000 INFO @ Wed, 22 Apr 2020 10:15:20: 32000000 INFO @ Wed, 22 Apr 2020 10:15:22: 39000000 INFO @ Wed, 22 Apr 2020 10:15:23: 26000000 INFO @ Wed, 22 Apr 2020 10:15:25: 33000000 INFO @ Wed, 22 Apr 2020 10:15:26: 40000000 INFO @ Wed, 22 Apr 2020 10:15:28: 27000000 INFO @ Wed, 22 Apr 2020 10:15:29: 34000000 INFO @ Wed, 22 Apr 2020 10:15:31: 41000000 INFO @ Wed, 22 Apr 2020 10:15:32: 28000000 INFO @ Wed, 22 Apr 2020 10:15:34: 35000000 INFO @ Wed, 22 Apr 2020 10:15:35: 42000000 INFO @ Wed, 22 Apr 2020 10:15:37: 29000000 INFO @ Wed, 22 Apr 2020 10:15:38: 36000000 INFO @ Wed, 22 Apr 2020 10:15:40: 43000000 INFO @ Wed, 22 Apr 2020 10:15:41: 30000000 INFO @ Wed, 22 Apr 2020 10:15:43: 37000000 INFO @ Wed, 22 Apr 2020 10:15:44: 44000000 INFO @ Wed, 22 Apr 2020 10:15:46: 31000000 INFO @ Wed, 22 Apr 2020 10:15:47: 38000000 INFO @ Wed, 22 Apr 2020 10:15:49: 45000000 INFO @ Wed, 22 Apr 2020 10:15:49: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:15:49: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:15:49: #1 total tags in treatment: 22347162 INFO @ Wed, 22 Apr 2020 10:15:49: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:15:49: #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 10:15:50: #1 tags after filtering in treatment: 13145811 INFO @ Wed, 22 Apr 2020 10:15:50: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 10:15:50: #1 finished! INFO @ Wed, 22 Apr 2020 10:15:50: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:15:50: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:15:50: 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 10:15:50: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:15:50: 32000000 INFO @ Wed, 22 Apr 2020 10:15:52: 39000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.05_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/SRX7409565/SRX7409565.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:15:55: 33000000 INFO @ Wed, 22 Apr 2020 10:15:56: 40000000 INFO @ Wed, 22 Apr 2020 10:15:59: 34000000 INFO @ Wed, 22 Apr 2020 10:16:01: 41000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:16:04: 35000000 INFO @ Wed, 22 Apr 2020 10:16:05: 42000000 INFO @ Wed, 22 Apr 2020 10:16:09: 36000000 INFO @ Wed, 22 Apr 2020 10:16:10: 43000000 INFO @ Wed, 22 Apr 2020 10:16:13: 37000000 INFO @ Wed, 22 Apr 2020 10:16:14: 44000000 INFO @ Wed, 22 Apr 2020 10:16:18: 38000000 INFO @ Wed, 22 Apr 2020 10:16:19: 45000000 INFO @ Wed, 22 Apr 2020 10:16:19: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:16:19: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:16:19: #1 total tags in treatment: 22347162 INFO @ Wed, 22 Apr 2020 10:16:19: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:16:19: #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 10:16:20: #1 tags after filtering in treatment: 13145811 INFO @ Wed, 22 Apr 2020 10:16:20: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 10:16:20: #1 finished! INFO @ Wed, 22 Apr 2020 10:16:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:16:20: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:16:20: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:16:20: 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 10:16:20: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:16:22: 39000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.10_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/SRX7409565/SRX7409565.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:16:27: 40000000 INFO @ Wed, 22 Apr 2020 10:16:31: 41000000 INFO @ Wed, 22 Apr 2020 10:16:35: 42000000 INFO @ Wed, 22 Apr 2020 10:16:40: 43000000 INFO @ Wed, 22 Apr 2020 10:16:44: 44000000 INFO @ Wed, 22 Apr 2020 10:16:48: 45000000 INFO @ Wed, 22 Apr 2020 10:16:49: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:16:49: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:16:49: #1 total tags in treatment: 22347162 INFO @ Wed, 22 Apr 2020 10:16:49: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:16:49: #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 10:16:49: #1 tags after filtering in treatment: 13145811 INFO @ Wed, 22 Apr 2020 10:16:49: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 10:16:49: #1 finished! INFO @ Wed, 22 Apr 2020 10:16:49: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:16:50: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:16:50: 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 10:16:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.20_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/SRX7409565/SRX7409565.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409565/SRX7409565.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling