Job ID = 5791669 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 ) 2020-04-22T01:23:28 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 ) 2020-04-22T01:23:28 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 ) 2020-04-22T01:23:28 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 ) 2020-04-22T01:24:53 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 ) 2020-04-22T01:32:05 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 : 27,978,796 reads read : 55,957,592 reads written : 55,957,592 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: 00:21:09 27978796 reads; of these: 27978796 (100.00%) were paired; of these: 2307449 (8.25%) aligned concordantly 0 times 21188742 (75.73%) aligned concordantly exactly 1 time 4482605 (16.02%) aligned concordantly >1 times ---- 2307449 pairs aligned concordantly 0 times; of these: 13395 (0.58%) aligned discordantly 1 time ---- 2294054 pairs aligned 0 times concordantly or discordantly; of these: 4588108 mates make up the pairs; of these: 4199379 (91.53%) aligned 0 times 280385 (6.11%) aligned exactly 1 time 108344 (2.36%) aligned >1 times 92.50% overall alignment rate Time searching: 00:21:09 Overall time: 00:21:09 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 24 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] 11526582 / 25678089 = 0.4489 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 11:06:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.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 11:06:58: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:06:58: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:07:03: 1000000 INFO @ Wed, 22 Apr 2020 11:07:08: 2000000 INFO @ Wed, 22 Apr 2020 11:07:13: 3000000 INFO @ Wed, 22 Apr 2020 11:07:18: 4000000 INFO @ Wed, 22 Apr 2020 11:07:23: 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 11:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.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 11:07:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:07:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:07:28: 6000000 INFO @ Wed, 22 Apr 2020 11:07:33: 1000000 INFO @ Wed, 22 Apr 2020 11:07:34: 7000000 INFO @ Wed, 22 Apr 2020 11:07:39: 2000000 INFO @ Wed, 22 Apr 2020 11:07:40: 8000000 INFO @ Wed, 22 Apr 2020 11:07:45: 3000000 INFO @ Wed, 22 Apr 2020 11:07:46: 9000000 INFO @ Wed, 22 Apr 2020 11:07:51: 4000000 INFO @ Wed, 22 Apr 2020 11:07:52: 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 11:07:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.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 11:07:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:07:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:07:58: 5000000 INFO @ Wed, 22 Apr 2020 11:07:58: 11000000 INFO @ Wed, 22 Apr 2020 11:08:04: 1000000 INFO @ Wed, 22 Apr 2020 11:08:04: 6000000 INFO @ Wed, 22 Apr 2020 11:08:04: 12000000 INFO @ Wed, 22 Apr 2020 11:08:10: 2000000 INFO @ Wed, 22 Apr 2020 11:08:10: 7000000 INFO @ Wed, 22 Apr 2020 11:08:10: 13000000 INFO @ Wed, 22 Apr 2020 11:08:16: 8000000 INFO @ Wed, 22 Apr 2020 11:08:16: 3000000 INFO @ Wed, 22 Apr 2020 11:08:16: 14000000 INFO @ Wed, 22 Apr 2020 11:08:22: 9000000 INFO @ Wed, 22 Apr 2020 11:08:22: 4000000 INFO @ Wed, 22 Apr 2020 11:08:22: 15000000 INFO @ Wed, 22 Apr 2020 11:08:28: 10000000 INFO @ Wed, 22 Apr 2020 11:08:28: 5000000 INFO @ Wed, 22 Apr 2020 11:08:28: 16000000 INFO @ Wed, 22 Apr 2020 11:08:35: 11000000 INFO @ Wed, 22 Apr 2020 11:08:35: 17000000 INFO @ Wed, 22 Apr 2020 11:08:35: 6000000 INFO @ Wed, 22 Apr 2020 11:08:41: 12000000 INFO @ Wed, 22 Apr 2020 11:08:41: 18000000 INFO @ Wed, 22 Apr 2020 11:08:41: 7000000 INFO @ Wed, 22 Apr 2020 11:08:48: 13000000 INFO @ Wed, 22 Apr 2020 11:08:48: 19000000 INFO @ Wed, 22 Apr 2020 11:08:49: 8000000 INFO @ Wed, 22 Apr 2020 11:08:54: 14000000 INFO @ Wed, 22 Apr 2020 11:08:54: 20000000 INFO @ Wed, 22 Apr 2020 11:08:55: 9000000 INFO @ Wed, 22 Apr 2020 11:09:01: 15000000 INFO @ Wed, 22 Apr 2020 11:09:01: 21000000 INFO @ Wed, 22 Apr 2020 11:09:02: 10000000 INFO @ Wed, 22 Apr 2020 11:09:07: 16000000 INFO @ Wed, 22 Apr 2020 11:09:07: 22000000 INFO @ Wed, 22 Apr 2020 11:09:08: 11000000 INFO @ Wed, 22 Apr 2020 11:09:14: 17000000 INFO @ Wed, 22 Apr 2020 11:09:14: 23000000 INFO @ Wed, 22 Apr 2020 11:09:15: 12000000 INFO @ Wed, 22 Apr 2020 11:09:20: 18000000 INFO @ Wed, 22 Apr 2020 11:09:20: 24000000 INFO @ Wed, 22 Apr 2020 11:09:22: 13000000 INFO @ Wed, 22 Apr 2020 11:09:27: 19000000 INFO @ Wed, 22 Apr 2020 11:09:27: 25000000 INFO @ Wed, 22 Apr 2020 11:09:28: 14000000 INFO @ Wed, 22 Apr 2020 11:09:33: 20000000 INFO @ Wed, 22 Apr 2020 11:09:33: 26000000 INFO @ Wed, 22 Apr 2020 11:09:35: 15000000 INFO @ Wed, 22 Apr 2020 11:09:39: 21000000 INFO @ Wed, 22 Apr 2020 11:09:40: 27000000 INFO @ Wed, 22 Apr 2020 11:09:41: 16000000 INFO @ Wed, 22 Apr 2020 11:09:46: 22000000 INFO @ Wed, 22 Apr 2020 11:09:46: 28000000 INFO @ Wed, 22 Apr 2020 11:09:48: 17000000 INFO @ Wed, 22 Apr 2020 11:09:51: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:09:51: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:09:51: #1 total tags in treatment: 14147462 INFO @ Wed, 22 Apr 2020 11:09:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:09:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:09:51: #1 tags after filtering in treatment: 7384415 INFO @ Wed, 22 Apr 2020 11:09:51: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Apr 2020 11:09:51: #1 finished! INFO @ Wed, 22 Apr 2020 11:09:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:09:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:09:51: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:09:51: 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 11:09:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.05_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/SRX7409630/SRX7409630.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:09:52: 23000000 INFO @ Wed, 22 Apr 2020 11:09:54: 18000000 INFO @ Wed, 22 Apr 2020 11:09:58: 24000000 INFO @ Wed, 22 Apr 2020 11:10:01: 19000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:10:05: 25000000 INFO @ Wed, 22 Apr 2020 11:10:08: 20000000 INFO @ Wed, 22 Apr 2020 11:10:11: 26000000 INFO @ Wed, 22 Apr 2020 11:10:14: 21000000 INFO @ Wed, 22 Apr 2020 11:10:17: 27000000 INFO @ Wed, 22 Apr 2020 11:10:20: 22000000 INFO @ Wed, 22 Apr 2020 11:10:23: 28000000 INFO @ Wed, 22 Apr 2020 11:10:27: 23000000 INFO @ Wed, 22 Apr 2020 11:10:28: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:10:28: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:10:28: #1 total tags in treatment: 14147462 INFO @ Wed, 22 Apr 2020 11:10:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:10:28: #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 11:10:28: #1 tags after filtering in treatment: 7384415 INFO @ Wed, 22 Apr 2020 11:10:28: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Apr 2020 11:10:28: #1 finished! INFO @ Wed, 22 Apr 2020 11:10:28: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:10:28: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:10:28: 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 11:10:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.10_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/SRX7409630/SRX7409630.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:10:33: 24000000 INFO @ Wed, 22 Apr 2020 11:10:38: 25000000 INFO @ Wed, 22 Apr 2020 11:10:44: 26000000 INFO @ Wed, 22 Apr 2020 11:10:50: 27000000 INFO @ Wed, 22 Apr 2020 11:10:56: 28000000 INFO @ Wed, 22 Apr 2020 11:11:00: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:11:00: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:11:00: #1 total tags in treatment: 14147462 INFO @ Wed, 22 Apr 2020 11:11:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:11:00: #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 11:11:00: #1 tags after filtering in treatment: 7384415 INFO @ Wed, 22 Apr 2020 11:11:00: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Apr 2020 11:11:00: #1 finished! INFO @ Wed, 22 Apr 2020 11:11:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:11:01: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:11:01: 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 11:11:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.20_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/SRX7409630/SRX7409630.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409630/SRX7409630.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling