Job ID = 5791288 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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 ) 2020-04-22T00:39:38 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 ) 2020-04-22T00:39:38 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 ) 2020-04-22T00:41:46 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 ) 2020-04-22T00:41:46 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 : 35,079,972 reads read : 70,159,944 reads written : 70,159,944 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: 00:18:32 35079972 reads; of these: 35079972 (100.00%) were paired; of these: 1078211 (3.07%) aligned concordantly 0 times 30072930 (85.73%) aligned concordantly exactly 1 time 3928831 (11.20%) aligned concordantly >1 times ---- 1078211 pairs aligned concordantly 0 times; of these: 59429 (5.51%) aligned discordantly 1 time ---- 1018782 pairs aligned 0 times concordantly or discordantly; of these: 2037564 mates make up the pairs; of these: 1625694 (79.79%) aligned 0 times 341025 (16.74%) aligned exactly 1 time 70845 (3.48%) aligned >1 times 97.68% overall alignment rate Time searching: 00:18:32 Overall time: 00:18:32 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] 11049265 / 34015453 = 0.3248 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 10:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.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 10:24:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:24:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:24:22: 1000000 INFO @ Wed, 22 Apr 2020 10:24:27: 2000000 INFO @ Wed, 22 Apr 2020 10:24:31: 3000000 INFO @ Wed, 22 Apr 2020 10:24:36: 4000000 INFO @ Wed, 22 Apr 2020 10:24:40: 5000000 INFO @ Wed, 22 Apr 2020 10:24:45: 6000000 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 10:24:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.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 10:24:47: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:24:47: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:24:49: 7000000 INFO @ Wed, 22 Apr 2020 10:24:52: 1000000 INFO @ Wed, 22 Apr 2020 10:24:54: 8000000 INFO @ Wed, 22 Apr 2020 10:24:57: 2000000 INFO @ Wed, 22 Apr 2020 10:24:59: 9000000 INFO @ Wed, 22 Apr 2020 10:25:02: 3000000 INFO @ Wed, 22 Apr 2020 10:25:04: 10000000 INFO @ Wed, 22 Apr 2020 10:25:07: 4000000 INFO @ Wed, 22 Apr 2020 10:25:09: 11000000 INFO @ Wed, 22 Apr 2020 10:25:12: 5000000 INFO @ Wed, 22 Apr 2020 10:25:14: 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 10:25:17: 6000000 INFO @ Wed, 22 Apr 2020 10:25:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.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 10:25:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:25:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:25:19: 13000000 INFO @ Wed, 22 Apr 2020 10:25:22: 7000000 INFO @ Wed, 22 Apr 2020 10:25:24: 1000000 INFO @ Wed, 22 Apr 2020 10:25:24: 14000000 INFO @ Wed, 22 Apr 2020 10:25:27: 8000000 INFO @ Wed, 22 Apr 2020 10:25:29: 15000000 INFO @ Wed, 22 Apr 2020 10:25:30: 2000000 INFO @ Wed, 22 Apr 2020 10:25:32: 9000000 INFO @ Wed, 22 Apr 2020 10:25:34: 16000000 INFO @ Wed, 22 Apr 2020 10:25:36: 3000000 INFO @ Wed, 22 Apr 2020 10:25:37: 10000000 INFO @ Wed, 22 Apr 2020 10:25:39: 17000000 INFO @ Wed, 22 Apr 2020 10:25:42: 4000000 INFO @ Wed, 22 Apr 2020 10:25:43: 11000000 INFO @ Wed, 22 Apr 2020 10:25:44: 18000000 INFO @ Wed, 22 Apr 2020 10:25:48: 5000000 INFO @ Wed, 22 Apr 2020 10:25:48: 12000000 INFO @ Wed, 22 Apr 2020 10:25:49: 19000000 INFO @ Wed, 22 Apr 2020 10:25:53: 13000000 INFO @ Wed, 22 Apr 2020 10:25:54: 6000000 INFO @ Wed, 22 Apr 2020 10:25:55: 20000000 INFO @ Wed, 22 Apr 2020 10:25:58: 14000000 INFO @ Wed, 22 Apr 2020 10:26:00: 21000000 INFO @ Wed, 22 Apr 2020 10:26:00: 7000000 INFO @ Wed, 22 Apr 2020 10:26:03: 15000000 INFO @ Wed, 22 Apr 2020 10:26:05: 22000000 INFO @ Wed, 22 Apr 2020 10:26:06: 8000000 INFO @ Wed, 22 Apr 2020 10:26:09: 16000000 INFO @ Wed, 22 Apr 2020 10:26:10: 23000000 INFO @ Wed, 22 Apr 2020 10:26:12: 9000000 INFO @ Wed, 22 Apr 2020 10:26:14: 17000000 INFO @ Wed, 22 Apr 2020 10:26:15: 24000000 INFO @ Wed, 22 Apr 2020 10:26:18: 10000000 INFO @ Wed, 22 Apr 2020 10:26:19: 18000000 INFO @ Wed, 22 Apr 2020 10:26:20: 25000000 INFO @ Wed, 22 Apr 2020 10:26:24: 19000000 INFO @ Wed, 22 Apr 2020 10:26:24: 11000000 INFO @ Wed, 22 Apr 2020 10:26:25: 26000000 INFO @ Wed, 22 Apr 2020 10:26:29: 20000000 INFO @ Wed, 22 Apr 2020 10:26:30: 12000000 INFO @ Wed, 22 Apr 2020 10:26:31: 27000000 INFO @ Wed, 22 Apr 2020 10:26:34: 21000000 INFO @ Wed, 22 Apr 2020 10:26:36: 28000000 INFO @ Wed, 22 Apr 2020 10:26:36: 13000000 INFO @ Wed, 22 Apr 2020 10:26:40: 22000000 INFO @ Wed, 22 Apr 2020 10:26:41: 29000000 INFO @ Wed, 22 Apr 2020 10:26:42: 14000000 INFO @ Wed, 22 Apr 2020 10:26:45: 23000000 INFO @ Wed, 22 Apr 2020 10:26:46: 30000000 INFO @ Wed, 22 Apr 2020 10:26:48: 15000000 INFO @ Wed, 22 Apr 2020 10:26:50: 24000000 INFO @ Wed, 22 Apr 2020 10:26:51: 31000000 INFO @ Wed, 22 Apr 2020 10:26:53: 16000000 INFO @ Wed, 22 Apr 2020 10:26:55: 25000000 INFO @ Wed, 22 Apr 2020 10:26:56: 32000000 INFO @ Wed, 22 Apr 2020 10:26:59: 17000000 INFO @ Wed, 22 Apr 2020 10:27:00: 26000000 INFO @ Wed, 22 Apr 2020 10:27:01: 33000000 INFO @ Wed, 22 Apr 2020 10:27:05: 27000000 INFO @ Wed, 22 Apr 2020 10:27:05: 18000000 INFO @ Wed, 22 Apr 2020 10:27:07: 34000000 INFO @ Wed, 22 Apr 2020 10:27:10: 28000000 INFO @ Wed, 22 Apr 2020 10:27:11: 19000000 INFO @ Wed, 22 Apr 2020 10:27:12: 35000000 INFO @ Wed, 22 Apr 2020 10:27:15: 29000000 INFO @ Wed, 22 Apr 2020 10:27:17: 20000000 INFO @ Wed, 22 Apr 2020 10:27:17: 36000000 INFO @ Wed, 22 Apr 2020 10:27:20: 30000000 INFO @ Wed, 22 Apr 2020 10:27:22: 37000000 INFO @ Wed, 22 Apr 2020 10:27:23: 21000000 INFO @ Wed, 22 Apr 2020 10:27:25: 31000000 INFO @ Wed, 22 Apr 2020 10:27:27: 38000000 INFO @ Wed, 22 Apr 2020 10:27:29: 22000000 INFO @ Wed, 22 Apr 2020 10:27:31: 32000000 INFO @ Wed, 22 Apr 2020 10:27:33: 39000000 INFO @ Wed, 22 Apr 2020 10:27:34: 23000000 INFO @ Wed, 22 Apr 2020 10:27:36: 33000000 INFO @ Wed, 22 Apr 2020 10:27:38: 40000000 INFO @ Wed, 22 Apr 2020 10:27:40: 24000000 INFO @ Wed, 22 Apr 2020 10:27:41: 34000000 INFO @ Wed, 22 Apr 2020 10:27:43: 41000000 INFO @ Wed, 22 Apr 2020 10:27:46: 25000000 INFO @ Wed, 22 Apr 2020 10:27:46: 35000000 INFO @ Wed, 22 Apr 2020 10:27:48: 42000000 INFO @ Wed, 22 Apr 2020 10:27:51: 36000000 INFO @ Wed, 22 Apr 2020 10:27:52: 26000000 INFO @ Wed, 22 Apr 2020 10:27:53: 43000000 INFO @ Wed, 22 Apr 2020 10:27:56: 37000000 INFO @ Wed, 22 Apr 2020 10:27:58: 27000000 INFO @ Wed, 22 Apr 2020 10:27:58: 44000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:28:02: 38000000 INFO @ Wed, 22 Apr 2020 10:28:03: 45000000 INFO @ Wed, 22 Apr 2020 10:28:04: 28000000 INFO @ Wed, 22 Apr 2020 10:28:07: 39000000 INFO @ Wed, 22 Apr 2020 10:28:09: 46000000 INFO @ Wed, 22 Apr 2020 10:28:09: 29000000 INFO @ Wed, 22 Apr 2020 10:28:11: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:28:11: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:28:11: #1 total tags in treatment: 22957032 INFO @ Wed, 22 Apr 2020 10:28:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:28:11: #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 10:28:11: #1 tags after filtering in treatment: 13380847 INFO @ Wed, 22 Apr 2020 10:28:11: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Apr 2020 10:28:11: #1 finished! INFO @ Wed, 22 Apr 2020 10:28:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:28:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:28:12: 40000000 INFO @ Wed, 22 Apr 2020 10:28:12: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:28:12: 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 10:28:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.05_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/SRX7409547/SRX7409547.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:28:15: 30000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:28:17: 41000000 INFO @ Wed, 22 Apr 2020 10:28:21: 31000000 INFO @ Wed, 22 Apr 2020 10:28:22: 42000000 INFO @ Wed, 22 Apr 2020 10:28:27: 32000000 INFO @ Wed, 22 Apr 2020 10:28:27: 43000000 INFO @ Wed, 22 Apr 2020 10:28:32: 44000000 INFO @ Wed, 22 Apr 2020 10:28:32: 33000000 INFO @ Wed, 22 Apr 2020 10:28:37: 45000000 INFO @ Wed, 22 Apr 2020 10:28:38: 34000000 INFO @ Wed, 22 Apr 2020 10:28:42: 46000000 INFO @ Wed, 22 Apr 2020 10:28:44: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:28:44: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:28:44: #1 total tags in treatment: 22957032 INFO @ Wed, 22 Apr 2020 10:28:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:28:44: #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 10:28:44: 35000000 INFO @ Wed, 22 Apr 2020 10:28:45: #1 tags after filtering in treatment: 13380847 INFO @ Wed, 22 Apr 2020 10:28:45: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Apr 2020 10:28:45: #1 finished! INFO @ Wed, 22 Apr 2020 10:28:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:28:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:28:45: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:28:45: 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 10:28:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.10_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/SRX7409547/SRX7409547.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:28:50: 36000000 INFO @ Wed, 22 Apr 2020 10:28:56: 37000000 INFO @ Wed, 22 Apr 2020 10:29:01: 38000000 INFO @ Wed, 22 Apr 2020 10:29:07: 39000000 INFO @ Wed, 22 Apr 2020 10:29:12: 40000000 INFO @ Wed, 22 Apr 2020 10:29:18: 41000000 INFO @ Wed, 22 Apr 2020 10:29:23: 42000000 INFO @ Wed, 22 Apr 2020 10:29:29: 43000000 INFO @ Wed, 22 Apr 2020 10:29:34: 44000000 INFO @ Wed, 22 Apr 2020 10:29:40: 45000000 INFO @ Wed, 22 Apr 2020 10:29:45: 46000000 INFO @ Wed, 22 Apr 2020 10:29:47: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:29:47: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:29:47: #1 total tags in treatment: 22957032 INFO @ Wed, 22 Apr 2020 10:29:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:29:47: #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 10:29:48: #1 tags after filtering in treatment: 13380847 INFO @ Wed, 22 Apr 2020 10:29:48: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Apr 2020 10:29:48: #1 finished! INFO @ Wed, 22 Apr 2020 10:29:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:29:49: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:29:49: 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 10:29:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.20_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/SRX7409547/SRX7409547.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409547/SRX7409547.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling