Job ID = 5791493 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:37:45 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 ) 2020-04-22T00:37:45 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 ) 2020-04-22T00:43:56 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 ) 2020-04-22T00:43:56 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 ) 2020-04-22T00:50:48 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 ) 2020-04-22T00:50:48 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 : 29,892,178 reads read : 59,784,356 reads written : 59,784,356 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: 00:16:07 29892178 reads; of these: 29892178 (100.00%) were paired; of these: 348200 (1.16%) aligned concordantly 0 times 26572377 (88.89%) aligned concordantly exactly 1 time 2971601 (9.94%) aligned concordantly >1 times ---- 348200 pairs aligned concordantly 0 times; of these: 96087 (27.60%) aligned discordantly 1 time ---- 252113 pairs aligned 0 times concordantly or discordantly; of these: 504226 mates make up the pairs; of these: 315309 (62.53%) aligned 0 times 137992 (27.37%) aligned exactly 1 time 50925 (10.10%) aligned >1 times 99.47% overall alignment rate Time searching: 00:16:07 Overall time: 00:16:07 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] 6154292 / 29557693 = 0.2082 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 10:23:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.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 10:23:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:23:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:23:09: 1000000 INFO @ Wed, 22 Apr 2020 10:23:14: 2000000 INFO @ Wed, 22 Apr 2020 10:23:19: 3000000 INFO @ Wed, 22 Apr 2020 10:23:24: 4000000 INFO @ Wed, 22 Apr 2020 10:23:29: 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 10:23:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.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 10:23:33: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:23:33: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:23:34: 6000000 INFO @ Wed, 22 Apr 2020 10:23:39: 1000000 INFO @ Wed, 22 Apr 2020 10:23:40: 7000000 INFO @ Wed, 22 Apr 2020 10:23:45: 2000000 INFO @ Wed, 22 Apr 2020 10:23:46: 8000000 INFO @ Wed, 22 Apr 2020 10:23:51: 3000000 INFO @ Wed, 22 Apr 2020 10:23:52: 9000000 INFO @ Wed, 22 Apr 2020 10:23:57: 4000000 INFO @ Wed, 22 Apr 2020 10:23:58: 10000000 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 10:24:03: 5000000 INFO @ Wed, 22 Apr 2020 10:24:04: 11000000 INFO @ Wed, 22 Apr 2020 10:24:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.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 10:24:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:24:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:24:10: 6000000 INFO @ Wed, 22 Apr 2020 10:24:10: 12000000 INFO @ Wed, 22 Apr 2020 10:24:11: 1000000 INFO @ Wed, 22 Apr 2020 10:24:16: 7000000 INFO @ Wed, 22 Apr 2020 10:24:17: 13000000 INFO @ Wed, 22 Apr 2020 10:24:19: 2000000 INFO @ Wed, 22 Apr 2020 10:24:23: 8000000 INFO @ Wed, 22 Apr 2020 10:24:24: 14000000 INFO @ Wed, 22 Apr 2020 10:24:26: 3000000 INFO @ Wed, 22 Apr 2020 10:24:30: 9000000 INFO @ Wed, 22 Apr 2020 10:24:30: 15000000 INFO @ Wed, 22 Apr 2020 10:24:33: 4000000 INFO @ Wed, 22 Apr 2020 10:24:36: 10000000 INFO @ Wed, 22 Apr 2020 10:24:37: 16000000 INFO @ Wed, 22 Apr 2020 10:24:40: 5000000 INFO @ Wed, 22 Apr 2020 10:24:43: 11000000 INFO @ Wed, 22 Apr 2020 10:24:44: 17000000 INFO @ Wed, 22 Apr 2020 10:24:47: 6000000 INFO @ Wed, 22 Apr 2020 10:24:50: 12000000 INFO @ Wed, 22 Apr 2020 10:24:50: 18000000 INFO @ Wed, 22 Apr 2020 10:24:54: 7000000 INFO @ Wed, 22 Apr 2020 10:24:56: 13000000 INFO @ Wed, 22 Apr 2020 10:24:57: 19000000 INFO @ Wed, 22 Apr 2020 10:25:01: 8000000 INFO @ Wed, 22 Apr 2020 10:25:03: 14000000 INFO @ Wed, 22 Apr 2020 10:25:04: 20000000 INFO @ Wed, 22 Apr 2020 10:25:09: 9000000 INFO @ Wed, 22 Apr 2020 10:25:10: 15000000 INFO @ Wed, 22 Apr 2020 10:25:11: 21000000 INFO @ Wed, 22 Apr 2020 10:25:16: 10000000 INFO @ Wed, 22 Apr 2020 10:25:17: 16000000 INFO @ Wed, 22 Apr 2020 10:25:17: 22000000 INFO @ Wed, 22 Apr 2020 10:25:23: 11000000 INFO @ Wed, 22 Apr 2020 10:25:23: 17000000 INFO @ Wed, 22 Apr 2020 10:25:24: 23000000 INFO @ Wed, 22 Apr 2020 10:25:30: 12000000 INFO @ Wed, 22 Apr 2020 10:25:30: 18000000 INFO @ Wed, 22 Apr 2020 10:25:31: 24000000 INFO @ Wed, 22 Apr 2020 10:25:37: 19000000 INFO @ Wed, 22 Apr 2020 10:25:37: 13000000 INFO @ Wed, 22 Apr 2020 10:25:38: 25000000 INFO @ Wed, 22 Apr 2020 10:25:44: 20000000 INFO @ Wed, 22 Apr 2020 10:25:44: 14000000 INFO @ Wed, 22 Apr 2020 10:25:44: 26000000 INFO @ Wed, 22 Apr 2020 10:25:50: 21000000 INFO @ Wed, 22 Apr 2020 10:25:51: 27000000 INFO @ Wed, 22 Apr 2020 10:25:51: 15000000 INFO @ Wed, 22 Apr 2020 10:25:57: 22000000 INFO @ Wed, 22 Apr 2020 10:25:58: 28000000 INFO @ Wed, 22 Apr 2020 10:25:58: 16000000 INFO @ Wed, 22 Apr 2020 10:26:04: 23000000 INFO @ Wed, 22 Apr 2020 10:26:04: 29000000 INFO @ Wed, 22 Apr 2020 10:26:06: 17000000 INFO @ Wed, 22 Apr 2020 10:26:10: 24000000 INFO @ Wed, 22 Apr 2020 10:26:11: 30000000 INFO @ Wed, 22 Apr 2020 10:26:13: 18000000 INFO @ Wed, 22 Apr 2020 10:26:17: 25000000 INFO @ Wed, 22 Apr 2020 10:26:18: 31000000 INFO @ Wed, 22 Apr 2020 10:26:21: 19000000 INFO @ Wed, 22 Apr 2020 10:26:24: 26000000 INFO @ Wed, 22 Apr 2020 10:26:24: 32000000 INFO @ Wed, 22 Apr 2020 10:26:28: 20000000 INFO @ Wed, 22 Apr 2020 10:26:30: 27000000 INFO @ Wed, 22 Apr 2020 10:26:31: 33000000 INFO @ Wed, 22 Apr 2020 10:26:35: 21000000 INFO @ Wed, 22 Apr 2020 10:26:37: 28000000 INFO @ Wed, 22 Apr 2020 10:26:38: 34000000 INFO @ Wed, 22 Apr 2020 10:26:42: 22000000 INFO @ Wed, 22 Apr 2020 10:26:44: 29000000 INFO @ Wed, 22 Apr 2020 10:26:45: 35000000 INFO @ Wed, 22 Apr 2020 10:26:49: 23000000 INFO @ Wed, 22 Apr 2020 10:26:51: 30000000 INFO @ Wed, 22 Apr 2020 10:26:51: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:26:57: 24000000 INFO @ Wed, 22 Apr 2020 10:26:57: 31000000 INFO @ Wed, 22 Apr 2020 10:26:58: 37000000 INFO @ Wed, 22 Apr 2020 10:27:04: 25000000 INFO @ Wed, 22 Apr 2020 10:27:04: 32000000 INFO @ Wed, 22 Apr 2020 10:27:05: 38000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:27:11: 33000000 INFO @ Wed, 22 Apr 2020 10:27:11: 26000000 INFO @ Wed, 22 Apr 2020 10:27:12: 39000000 INFO @ Wed, 22 Apr 2020 10:27:18: 34000000 INFO @ Wed, 22 Apr 2020 10:27:18: 40000000 INFO @ Wed, 22 Apr 2020 10:27:19: 27000000 INFO @ Wed, 22 Apr 2020 10:27:24: 35000000 INFO @ Wed, 22 Apr 2020 10:27:25: 41000000 INFO @ Wed, 22 Apr 2020 10:27:26: 28000000 INFO @ Wed, 22 Apr 2020 10:27:31: 36000000 INFO @ Wed, 22 Apr 2020 10:27:32: 42000000 INFO @ Wed, 22 Apr 2020 10:27:33: 29000000 INFO @ Wed, 22 Apr 2020 10:27:38: 37000000 INFO @ Wed, 22 Apr 2020 10:27:39: 43000000 INFO @ Wed, 22 Apr 2020 10:27:40: 30000000 INFO @ Wed, 22 Apr 2020 10:27:45: 38000000 INFO @ Wed, 22 Apr 2020 10:27:46: 44000000 INFO @ Wed, 22 Apr 2020 10:27:48: 31000000 INFO @ Wed, 22 Apr 2020 10:27:52: 39000000 INFO @ Wed, 22 Apr 2020 10:27:52: 45000000 INFO @ Wed, 22 Apr 2020 10:27:55: 32000000 INFO @ Wed, 22 Apr 2020 10:27:58: 40000000 INFO @ Wed, 22 Apr 2020 10:27:59: 46000000 INFO @ Wed, 22 Apr 2020 10:28:03: 33000000 INFO @ Wed, 22 Apr 2020 10:28:05: 41000000 INFO @ Wed, 22 Apr 2020 10:28:06: 47000000 INFO @ Wed, 22 Apr 2020 10:28:07: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:28:07: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:28:07: #1 total tags in treatment: 23391952 INFO @ Wed, 22 Apr 2020 10:28:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:28:07: #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 10:28:08: #1 tags after filtering in treatment: 13933963 INFO @ Wed, 22 Apr 2020 10:28:08: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 10:28:08: #1 finished! INFO @ Wed, 22 Apr 2020 10:28:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:28:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:28:08: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:28:08: 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 10:28:08: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:28:10: 34000000 INFO @ Wed, 22 Apr 2020 10:28:12: 42000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.05_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/SRX7409579/SRX7409579.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:28:17: 35000000 INFO @ Wed, 22 Apr 2020 10:28:18: 43000000 INFO @ Wed, 22 Apr 2020 10:28:25: 36000000 INFO @ Wed, 22 Apr 2020 10:28:25: 44000000 INFO @ Wed, 22 Apr 2020 10:28:32: 45000000 INFO @ Wed, 22 Apr 2020 10:28:32: 37000000 INFO @ Wed, 22 Apr 2020 10:28:38: 46000000 INFO @ Wed, 22 Apr 2020 10:28:39: 38000000 INFO @ Wed, 22 Apr 2020 10:28:45: 47000000 INFO @ Wed, 22 Apr 2020 10:28:46: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:28:46: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:28:46: #1 total tags in treatment: 23391952 INFO @ Wed, 22 Apr 2020 10:28:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:28:46: #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 10:28:46: 39000000 INFO @ Wed, 22 Apr 2020 10:28:46: #1 tags after filtering in treatment: 13933963 INFO @ Wed, 22 Apr 2020 10:28:46: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 10:28:46: #1 finished! INFO @ Wed, 22 Apr 2020 10:28:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:28:47: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:28:47: 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 10:28:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.10_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/SRX7409579/SRX7409579.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:28:53: 40000000 INFO @ Wed, 22 Apr 2020 10:28:59: 41000000 INFO @ Wed, 22 Apr 2020 10:29:06: 42000000 INFO @ Wed, 22 Apr 2020 10:29:12: 43000000 INFO @ Wed, 22 Apr 2020 10:29:19: 44000000 INFO @ Wed, 22 Apr 2020 10:29:25: 45000000 INFO @ Wed, 22 Apr 2020 10:29:32: 46000000 INFO @ Wed, 22 Apr 2020 10:29:38: 47000000 INFO @ Wed, 22 Apr 2020 10:29:39: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:29:39: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:29:39: #1 total tags in treatment: 23391952 INFO @ Wed, 22 Apr 2020 10:29:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:29:39: #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 10:29:40: #1 tags after filtering in treatment: 13933963 INFO @ Wed, 22 Apr 2020 10:29:40: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 10:29:40: #1 finished! INFO @ Wed, 22 Apr 2020 10:29:40: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:29:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:29:40: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:29:40: 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 10:29:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.20_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/SRX7409579/SRX7409579.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409579/SRX7409579.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling