Job ID = 5791657 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:21:43 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 ) 2020-04-22T01:21:43 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 ) 2020-04-22T01:21:43 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 ) 2020-04-22T01:21:43 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 : 20,694,038 reads read : 41,388,076 reads written : 41,388,076 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: 00:11:13 20694038 reads; of these: 20694038 (100.00%) were paired; of these: 544302 (2.63%) aligned concordantly 0 times 18275549 (88.31%) aligned concordantly exactly 1 time 1874187 (9.06%) aligned concordantly >1 times ---- 544302 pairs aligned concordantly 0 times; of these: 13090 (2.40%) aligned discordantly 1 time ---- 531212 pairs aligned 0 times concordantly or discordantly; of these: 1062424 mates make up the pairs; of these: 870901 (81.97%) aligned 0 times 163747 (15.41%) aligned exactly 1 time 27776 (2.61%) aligned >1 times 97.90% overall alignment rate Time searching: 00:11:14 Overall time: 00:11:14 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 20 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] 2944924 / 20153435 = 0.1461 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 10:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.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 10:43:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:43:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:43:09: 1000000 INFO @ Wed, 22 Apr 2020 10:43:14: 2000000 INFO @ Wed, 22 Apr 2020 10:43:19: 3000000 INFO @ Wed, 22 Apr 2020 10:43:24: 4000000 INFO @ Wed, 22 Apr 2020 10:43:28: 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 10:43:33: 6000000 INFO @ Wed, 22 Apr 2020 10:43:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.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 10:43:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:43:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:43:38: 7000000 INFO @ Wed, 22 Apr 2020 10:43:38: 1000000 INFO @ Wed, 22 Apr 2020 10:43:42: 2000000 INFO @ Wed, 22 Apr 2020 10:43:43: 8000000 INFO @ Wed, 22 Apr 2020 10:43:47: 3000000 INFO @ Wed, 22 Apr 2020 10:43:47: 9000000 INFO @ Wed, 22 Apr 2020 10:43:51: 4000000 INFO @ Wed, 22 Apr 2020 10:43:52: 10000000 INFO @ Wed, 22 Apr 2020 10:43:55: 5000000 INFO @ Wed, 22 Apr 2020 10:43:57: 11000000 INFO @ Wed, 22 Apr 2020 10:43:59: 6000000 INFO @ Wed, 22 Apr 2020 10:44:01: 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 10:44:03: 7000000 INFO @ Wed, 22 Apr 2020 10:44:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.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 10:44:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:44:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:44:06: 13000000 INFO @ Wed, 22 Apr 2020 10:44:07: 8000000 INFO @ Wed, 22 Apr 2020 10:44:08: 1000000 INFO @ Wed, 22 Apr 2020 10:44:11: 14000000 INFO @ Wed, 22 Apr 2020 10:44:12: 9000000 INFO @ Wed, 22 Apr 2020 10:44:12: 2000000 INFO @ Wed, 22 Apr 2020 10:44:15: 15000000 INFO @ Wed, 22 Apr 2020 10:44:16: 10000000 INFO @ Wed, 22 Apr 2020 10:44:16: 3000000 INFO @ Wed, 22 Apr 2020 10:44:20: 11000000 INFO @ Wed, 22 Apr 2020 10:44:20: 16000000 INFO @ Wed, 22 Apr 2020 10:44:21: 4000000 INFO @ Wed, 22 Apr 2020 10:44:24: 12000000 INFO @ Wed, 22 Apr 2020 10:44:25: 17000000 INFO @ Wed, 22 Apr 2020 10:44:25: 5000000 INFO @ Wed, 22 Apr 2020 10:44:28: 13000000 INFO @ Wed, 22 Apr 2020 10:44:29: 6000000 INFO @ Wed, 22 Apr 2020 10:44:29: 18000000 INFO @ Wed, 22 Apr 2020 10:44:32: 14000000 INFO @ Wed, 22 Apr 2020 10:44:33: 7000000 INFO @ Wed, 22 Apr 2020 10:44:34: 19000000 INFO @ Wed, 22 Apr 2020 10:44:36: 15000000 INFO @ Wed, 22 Apr 2020 10:44:37: 8000000 INFO @ Wed, 22 Apr 2020 10:44:39: 20000000 INFO @ Wed, 22 Apr 2020 10:44:40: 16000000 INFO @ Wed, 22 Apr 2020 10:44:41: 9000000 INFO @ Wed, 22 Apr 2020 10:44:43: 21000000 INFO @ Wed, 22 Apr 2020 10:44:44: 17000000 INFO @ Wed, 22 Apr 2020 10:44:45: 10000000 INFO @ Wed, 22 Apr 2020 10:44:48: 22000000 INFO @ Wed, 22 Apr 2020 10:44:48: 18000000 INFO @ Wed, 22 Apr 2020 10:44:50: 11000000 INFO @ Wed, 22 Apr 2020 10:44:52: 19000000 INFO @ Wed, 22 Apr 2020 10:44:53: 23000000 INFO @ Wed, 22 Apr 2020 10:44:54: 12000000 INFO @ Wed, 22 Apr 2020 10:44:57: 20000000 INFO @ Wed, 22 Apr 2020 10:44:57: 24000000 INFO @ Wed, 22 Apr 2020 10:44:58: 13000000 INFO @ Wed, 22 Apr 2020 10:45:01: 21000000 INFO @ Wed, 22 Apr 2020 10:45:02: 14000000 INFO @ Wed, 22 Apr 2020 10:45:02: 25000000 INFO @ Wed, 22 Apr 2020 10:45:05: 22000000 INFO @ Wed, 22 Apr 2020 10:45:06: 15000000 INFO @ Wed, 22 Apr 2020 10:45:07: 26000000 INFO @ Wed, 22 Apr 2020 10:45:09: 23000000 INFO @ Wed, 22 Apr 2020 10:45:10: 16000000 INFO @ Wed, 22 Apr 2020 10:45:12: 27000000 INFO @ Wed, 22 Apr 2020 10:45:13: 24000000 INFO @ Wed, 22 Apr 2020 10:45:14: 17000000 INFO @ Wed, 22 Apr 2020 10:45:16: 28000000 INFO @ Wed, 22 Apr 2020 10:45:17: 25000000 INFO @ Wed, 22 Apr 2020 10:45:18: 18000000 INFO @ Wed, 22 Apr 2020 10:45:21: 29000000 INFO @ Wed, 22 Apr 2020 10:45:21: 26000000 INFO @ Wed, 22 Apr 2020 10:45:23: 19000000 INFO @ Wed, 22 Apr 2020 10:45:25: 27000000 INFO @ Wed, 22 Apr 2020 10:45:26: 30000000 INFO @ Wed, 22 Apr 2020 10:45:27: 20000000 INFO @ Wed, 22 Apr 2020 10:45:29: 28000000 INFO @ Wed, 22 Apr 2020 10:45:30: 31000000 INFO @ Wed, 22 Apr 2020 10:45:31: 21000000 INFO @ Wed, 22 Apr 2020 10:45:33: 29000000 INFO @ Wed, 22 Apr 2020 10:45:35: 22000000 INFO @ Wed, 22 Apr 2020 10:45:35: 32000000 INFO @ Wed, 22 Apr 2020 10:45:37: 30000000 INFO @ Wed, 22 Apr 2020 10:45:39: 23000000 INFO @ Wed, 22 Apr 2020 10:45:40: 33000000 INFO @ Wed, 22 Apr 2020 10:45:42: 31000000 INFO @ Wed, 22 Apr 2020 10:45:43: 24000000 INFO @ Wed, 22 Apr 2020 10:45:44: 34000000 INFO @ Wed, 22 Apr 2020 10:45:46: 32000000 INFO @ Wed, 22 Apr 2020 10:45:47: 25000000 INFO @ Wed, 22 Apr 2020 10:45:47: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:45:47: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:45:47: #1 total tags in treatment: 17205372 INFO @ Wed, 22 Apr 2020 10:45:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:45:47: #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 10:45:48: #1 tags after filtering in treatment: 9974853 INFO @ Wed, 22 Apr 2020 10:45:48: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Apr 2020 10:45:48: #1 finished! INFO @ Wed, 22 Apr 2020 10:45:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:45:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:45:48: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:45:48: 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 10:45:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.05_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/SRX7409621/SRX7409621.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:45:50: 33000000 INFO @ Wed, 22 Apr 2020 10:45:51: 26000000 INFO @ Wed, 22 Apr 2020 10:45:54: 34000000 INFO @ Wed, 22 Apr 2020 10:45:55: 27000000 INFO @ Wed, 22 Apr 2020 10:45:57: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:45:57: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:45:57: #1 total tags in treatment: 17205372 INFO @ Wed, 22 Apr 2020 10:45:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:45:57: #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 10:45:57: #1 tags after filtering in treatment: 9974853 INFO @ Wed, 22 Apr 2020 10:45:57: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Apr 2020 10:45:57: #1 finished! INFO @ Wed, 22 Apr 2020 10:45:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:45:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:45:58: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:45:58: 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 10:45:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.10_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/SRX7409621/SRX7409621.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:45:59: 28000000 INFO @ Wed, 22 Apr 2020 10:46:03: 29000000 INFO @ Wed, 22 Apr 2020 10:46:07: 30000000 INFO @ Wed, 22 Apr 2020 10:46:11: 31000000 INFO @ Wed, 22 Apr 2020 10:46:15: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:46:20: 33000000 INFO @ Wed, 22 Apr 2020 10:46:24: 34000000 INFO @ Wed, 22 Apr 2020 10:46:26: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:46:26: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:46:26: #1 total tags in treatment: 17205372 INFO @ Wed, 22 Apr 2020 10:46:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:46:26: #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 10:46:27: #1 tags after filtering in treatment: 9974853 INFO @ Wed, 22 Apr 2020 10:46:27: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Apr 2020 10:46:27: #1 finished! INFO @ Wed, 22 Apr 2020 10:46:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:46:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:46:27: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:46:27: 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 10:46:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.20_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/SRX7409621/SRX7409621.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409621/SRX7409621.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。