Job ID = 5791644 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:00:38 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 ) 2020-04-22T01:00:38 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 ) 2020-04-22T01:00:38 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 ) 2020-04-22T01:00:38 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 ) 2020-04-22T01:10:28 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 ) spots read : 23,992,822 reads read : 47,985,644 reads written : 47,985,644 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: 00:12:57 23992822 reads; of these: 23992822 (100.00%) were paired; of these: 910800 (3.80%) aligned concordantly 0 times 21111513 (87.99%) aligned concordantly exactly 1 time 1970509 (8.21%) aligned concordantly >1 times ---- 910800 pairs aligned concordantly 0 times; of these: 32187 (3.53%) aligned discordantly 1 time ---- 878613 pairs aligned 0 times concordantly or discordantly; of these: 1757226 mates make up the pairs; of these: 1485586 (84.54%) aligned 0 times 236939 (13.48%) aligned exactly 1 time 34701 (1.97%) aligned >1 times 96.90% overall alignment rate Time searching: 00:12:57 Overall time: 00:12:57 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 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] 3347750 / 23087378 = 0.1450 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 10:36:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.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 10:36:10: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:36:10: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:36:14: 1000000 INFO @ Wed, 22 Apr 2020 10:36:18: 2000000 INFO @ Wed, 22 Apr 2020 10:36:23: 3000000 INFO @ Wed, 22 Apr 2020 10:36:27: 4000000 INFO @ Wed, 22 Apr 2020 10:36:32: 5000000 INFO @ Wed, 22 Apr 2020 10:36:36: 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 10:36:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.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 10:36:40: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:36:40: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:36:41: 7000000 INFO @ Wed, 22 Apr 2020 10:36:44: 1000000 INFO @ Wed, 22 Apr 2020 10:36:46: 8000000 INFO @ Wed, 22 Apr 2020 10:36:49: 2000000 INFO @ Wed, 22 Apr 2020 10:36:50: 9000000 INFO @ Wed, 22 Apr 2020 10:36:54: 3000000 INFO @ Wed, 22 Apr 2020 10:36:55: 10000000 INFO @ Wed, 22 Apr 2020 10:36:58: 4000000 INFO @ Wed, 22 Apr 2020 10:37:00: 11000000 INFO @ Wed, 22 Apr 2020 10:37:03: 5000000 INFO @ Wed, 22 Apr 2020 10:37:04: 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 10:37:08: 6000000 INFO @ Wed, 22 Apr 2020 10:37:09: 13000000 INFO @ Wed, 22 Apr 2020 10:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.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 10:37:09: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:37:09: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:37:13: 7000000 INFO @ Wed, 22 Apr 2020 10:37:14: 14000000 INFO @ Wed, 22 Apr 2020 10:37:15: 1000000 INFO @ Wed, 22 Apr 2020 10:37:17: 8000000 INFO @ Wed, 22 Apr 2020 10:37:19: 15000000 INFO @ Wed, 22 Apr 2020 10:37:19: 2000000 INFO @ Wed, 22 Apr 2020 10:37:22: 9000000 INFO @ Wed, 22 Apr 2020 10:37:23: 16000000 INFO @ Wed, 22 Apr 2020 10:37:24: 3000000 INFO @ Wed, 22 Apr 2020 10:37:27: 10000000 INFO @ Wed, 22 Apr 2020 10:37:28: 17000000 INFO @ Wed, 22 Apr 2020 10:37:29: 4000000 INFO @ Wed, 22 Apr 2020 10:37:31: 11000000 INFO @ Wed, 22 Apr 2020 10:37:33: 18000000 INFO @ Wed, 22 Apr 2020 10:37:34: 5000000 INFO @ Wed, 22 Apr 2020 10:37:36: 12000000 INFO @ Wed, 22 Apr 2020 10:37:38: 19000000 INFO @ Wed, 22 Apr 2020 10:37:38: 6000000 INFO @ Wed, 22 Apr 2020 10:37:41: 13000000 INFO @ Wed, 22 Apr 2020 10:37:42: 20000000 INFO @ Wed, 22 Apr 2020 10:37:43: 7000000 INFO @ Wed, 22 Apr 2020 10:37:46: 14000000 INFO @ Wed, 22 Apr 2020 10:37:47: 21000000 INFO @ Wed, 22 Apr 2020 10:37:48: 8000000 INFO @ Wed, 22 Apr 2020 10:37:50: 15000000 INFO @ Wed, 22 Apr 2020 10:37:52: 22000000 INFO @ Wed, 22 Apr 2020 10:37:53: 9000000 INFO @ Wed, 22 Apr 2020 10:37:55: 16000000 INFO @ Wed, 22 Apr 2020 10:37:57: 23000000 INFO @ Wed, 22 Apr 2020 10:37:58: 10000000 INFO @ Wed, 22 Apr 2020 10:38:00: 17000000 INFO @ Wed, 22 Apr 2020 10:38:01: 24000000 INFO @ Wed, 22 Apr 2020 10:38:02: 11000000 INFO @ Wed, 22 Apr 2020 10:38:04: 18000000 INFO @ Wed, 22 Apr 2020 10:38:06: 25000000 INFO @ Wed, 22 Apr 2020 10:38:07: 12000000 INFO @ Wed, 22 Apr 2020 10:38:09: 19000000 INFO @ Wed, 22 Apr 2020 10:38:11: 26000000 INFO @ Wed, 22 Apr 2020 10:38:12: 13000000 INFO @ Wed, 22 Apr 2020 10:38:14: 20000000 INFO @ Wed, 22 Apr 2020 10:38:15: 27000000 INFO @ Wed, 22 Apr 2020 10:38:17: 14000000 INFO @ Wed, 22 Apr 2020 10:38:18: 21000000 INFO @ Wed, 22 Apr 2020 10:38:20: 28000000 INFO @ Wed, 22 Apr 2020 10:38:21: 15000000 INFO @ Wed, 22 Apr 2020 10:38:23: 22000000 INFO @ Wed, 22 Apr 2020 10:38:25: 29000000 INFO @ Wed, 22 Apr 2020 10:38:26: 16000000 INFO @ Wed, 22 Apr 2020 10:38:27: 23000000 INFO @ Wed, 22 Apr 2020 10:38:30: 30000000 INFO @ Wed, 22 Apr 2020 10:38:31: 17000000 INFO @ Wed, 22 Apr 2020 10:38:32: 24000000 INFO @ Wed, 22 Apr 2020 10:38:34: 31000000 INFO @ Wed, 22 Apr 2020 10:38:36: 18000000 INFO @ Wed, 22 Apr 2020 10:38:37: 25000000 INFO @ Wed, 22 Apr 2020 10:38:39: 32000000 INFO @ Wed, 22 Apr 2020 10:38:40: 19000000 INFO @ Wed, 22 Apr 2020 10:38:42: 26000000 INFO @ Wed, 22 Apr 2020 10:38:44: 33000000 INFO @ Wed, 22 Apr 2020 10:38:45: 20000000 INFO @ Wed, 22 Apr 2020 10:38:46: 27000000 INFO @ Wed, 22 Apr 2020 10:38:49: 34000000 INFO @ Wed, 22 Apr 2020 10:38:50: 21000000 INFO @ Wed, 22 Apr 2020 10:38:51: 28000000 INFO @ Wed, 22 Apr 2020 10:38:53: 35000000 INFO @ Wed, 22 Apr 2020 10:38:54: 22000000 INFO @ Wed, 22 Apr 2020 10:38:56: 29000000 INFO @ Wed, 22 Apr 2020 10:38:58: 36000000 INFO @ Wed, 22 Apr 2020 10:38:59: 23000000 INFO @ Wed, 22 Apr 2020 10:39:00: 30000000 INFO @ Wed, 22 Apr 2020 10:39:03: 37000000 INFO @ Wed, 22 Apr 2020 10:39:04: 24000000 INFO @ Wed, 22 Apr 2020 10:39:05: 31000000 INFO @ Wed, 22 Apr 2020 10:39:07: 38000000 INFO @ Wed, 22 Apr 2020 10:39:09: 25000000 INFO @ Wed, 22 Apr 2020 10:39:10: 32000000 INFO @ Wed, 22 Apr 2020 10:39:12: 39000000 INFO @ Wed, 22 Apr 2020 10:39:13: 26000000 INFO @ Wed, 22 Apr 2020 10:39:14: 33000000 INFO @ Wed, 22 Apr 2020 10:39:16: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:39:16: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:39:16: #1 total tags in treatment: 19735034 INFO @ Wed, 22 Apr 2020 10:39:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:39:16: #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 10:39:16: #1 tags after filtering in treatment: 11009361 INFO @ Wed, 22 Apr 2020 10:39:16: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 22 Apr 2020 10:39:16: #1 finished! INFO @ Wed, 22 Apr 2020 10:39:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:39:17: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:39:17: 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 10:39:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.05_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/SRX7409608/SRX7409608.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:39:18: 27000000 INFO @ Wed, 22 Apr 2020 10:39:19: 34000000 INFO @ Wed, 22 Apr 2020 10:39:23: 28000000 INFO @ Wed, 22 Apr 2020 10:39:23: 35000000 INFO @ Wed, 22 Apr 2020 10:39:27: 29000000 INFO @ Wed, 22 Apr 2020 10:39:28: 36000000 INFO @ Wed, 22 Apr 2020 10:39:32: 30000000 INFO @ Wed, 22 Apr 2020 10:39:33: 37000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:39:37: 31000000 INFO @ Wed, 22 Apr 2020 10:39:37: 38000000 INFO @ Wed, 22 Apr 2020 10:39:41: 32000000 INFO @ Wed, 22 Apr 2020 10:39:42: 39000000 INFO @ Wed, 22 Apr 2020 10:39:46: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:39:46: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:39:46: #1 total tags in treatment: 19735034 INFO @ Wed, 22 Apr 2020 10:39:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:39:46: #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 10:39:46: 33000000 INFO @ Wed, 22 Apr 2020 10:39:46: #1 tags after filtering in treatment: 11009361 INFO @ Wed, 22 Apr 2020 10:39:46: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 22 Apr 2020 10:39:46: #1 finished! INFO @ Wed, 22 Apr 2020 10:39:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:39:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:39:47: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:39:47: 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 10:39:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.10_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/SRX7409608/SRX7409608.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:39:51: 34000000 INFO @ Wed, 22 Apr 2020 10:39:55: 35000000 INFO @ Wed, 22 Apr 2020 10:40:00: 36000000 INFO @ Wed, 22 Apr 2020 10:40:04: 37000000 INFO @ Wed, 22 Apr 2020 10:40:08: 38000000 INFO @ Wed, 22 Apr 2020 10:40:13: 39000000 INFO @ Wed, 22 Apr 2020 10:40:17: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:40:17: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:40:17: #1 total tags in treatment: 19735034 INFO @ Wed, 22 Apr 2020 10:40:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:40:17: #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 10:40:17: #1 tags after filtering in treatment: 11009361 INFO @ Wed, 22 Apr 2020 10:40:17: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 22 Apr 2020 10:40:17: #1 finished! INFO @ Wed, 22 Apr 2020 10:40:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:40:18: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:40:18: 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 10:40:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.20_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/SRX7409608/SRX7409608.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409608/SRX7409608.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling