Job ID = 5791676 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:36:36 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 ) 2020-04-22T01:36:36 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 ) 2020-04-22T01:36:36 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 ) 2020-04-22T01:36:36 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 ) 2020-04-22T01:36:36 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 ) 2020-04-22T01:41:35 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 ) 2020-04-22T01:46:34 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 : 18,933,332 reads read : 37,866,664 reads written : 37,866,664 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: 00:20:58 18933332 reads; of these: 18933332 (100.00%) were paired; of these: 4483145 (23.68%) aligned concordantly 0 times 12052885 (63.66%) aligned concordantly exactly 1 time 2397302 (12.66%) aligned concordantly >1 times ---- 4483145 pairs aligned concordantly 0 times; of these: 972495 (21.69%) aligned discordantly 1 time ---- 3510650 pairs aligned 0 times concordantly or discordantly; of these: 7021300 mates make up the pairs; of these: 6143372 (87.50%) aligned 0 times 359147 (5.12%) aligned exactly 1 time 518781 (7.39%) aligned >1 times 83.78% overall alignment rate Time searching: 00:20:58 Overall time: 00:20:58 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] 2384937 / 15361179 = 0.1553 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 11:34:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.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 11:34:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:34:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:34:09: 1000000 INFO @ Wed, 22 Apr 2020 11:34:16: 2000000 INFO @ Wed, 22 Apr 2020 11:34:24: 3000000 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 11:34:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.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 11:34:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:34:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:34:31: 4000000 INFO @ Wed, 22 Apr 2020 11:34:39: 5000000 INFO @ Wed, 22 Apr 2020 11:34:40: 1000000 INFO @ Wed, 22 Apr 2020 11:34:48: 6000000 INFO @ Wed, 22 Apr 2020 11:34:49: 2000000 INFO @ Wed, 22 Apr 2020 11:34:56: 7000000 INFO @ Wed, 22 Apr 2020 11:34:58: 3000000 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 11:35:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.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 11:35:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:35:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:35:05: 8000000 INFO @ Wed, 22 Apr 2020 11:35:06: 4000000 INFO @ Wed, 22 Apr 2020 11:35:11: 1000000 INFO @ Wed, 22 Apr 2020 11:35:14: 9000000 INFO @ Wed, 22 Apr 2020 11:35:15: 5000000 INFO @ Wed, 22 Apr 2020 11:35:20: 2000000 INFO @ Wed, 22 Apr 2020 11:35:22: 10000000 INFO @ Wed, 22 Apr 2020 11:35:24: 6000000 INFO @ Wed, 22 Apr 2020 11:35:30: 3000000 INFO @ Wed, 22 Apr 2020 11:35:31: 11000000 INFO @ Wed, 22 Apr 2020 11:35:33: 7000000 INFO @ Wed, 22 Apr 2020 11:35:39: 4000000 INFO @ Wed, 22 Apr 2020 11:35:40: 12000000 INFO @ Wed, 22 Apr 2020 11:35:43: 8000000 INFO @ Wed, 22 Apr 2020 11:35:48: 5000000 INFO @ Wed, 22 Apr 2020 11:35:49: 13000000 INFO @ Wed, 22 Apr 2020 11:35:52: 9000000 INFO @ Wed, 22 Apr 2020 11:35:57: 6000000 INFO @ Wed, 22 Apr 2020 11:35:58: 14000000 INFO @ Wed, 22 Apr 2020 11:36:01: 10000000 INFO @ Wed, 22 Apr 2020 11:36:07: 7000000 INFO @ Wed, 22 Apr 2020 11:36:07: 15000000 INFO @ Wed, 22 Apr 2020 11:36:10: 11000000 INFO @ Wed, 22 Apr 2020 11:36:16: 16000000 INFO @ Wed, 22 Apr 2020 11:36:16: 8000000 INFO @ Wed, 22 Apr 2020 11:36:19: 12000000 INFO @ Wed, 22 Apr 2020 11:36:25: 17000000 INFO @ Wed, 22 Apr 2020 11:36:26: 9000000 INFO @ Wed, 22 Apr 2020 11:36:28: 13000000 INFO @ Wed, 22 Apr 2020 11:36:34: 18000000 INFO @ Wed, 22 Apr 2020 11:36:35: 10000000 INFO @ Wed, 22 Apr 2020 11:36:37: 14000000 INFO @ Wed, 22 Apr 2020 11:36:43: 19000000 INFO @ Wed, 22 Apr 2020 11:36:45: 11000000 INFO @ Wed, 22 Apr 2020 11:36:46: 15000000 INFO @ Wed, 22 Apr 2020 11:36:52: 20000000 INFO @ Wed, 22 Apr 2020 11:36:54: 12000000 INFO @ Wed, 22 Apr 2020 11:36:55: 16000000 INFO @ Wed, 22 Apr 2020 11:37:01: 21000000 INFO @ Wed, 22 Apr 2020 11:37:03: 13000000 INFO @ Wed, 22 Apr 2020 11:37:04: 17000000 INFO @ Wed, 22 Apr 2020 11:37:10: 22000000 INFO @ Wed, 22 Apr 2020 11:37:12: 14000000 INFO @ Wed, 22 Apr 2020 11:37:13: 18000000 INFO @ Wed, 22 Apr 2020 11:37:20: 23000000 INFO @ Wed, 22 Apr 2020 11:37:22: 15000000 INFO @ Wed, 22 Apr 2020 11:37:22: 19000000 INFO @ Wed, 22 Apr 2020 11:37:29: 24000000 INFO @ Wed, 22 Apr 2020 11:37:31: 20000000 INFO @ Wed, 22 Apr 2020 11:37:31: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:37:38: 25000000 INFO @ Wed, 22 Apr 2020 11:37:40: 21000000 INFO @ Wed, 22 Apr 2020 11:37:40: 17000000 INFO @ Wed, 22 Apr 2020 11:37:47: 26000000 INFO @ Wed, 22 Apr 2020 11:37:49: 22000000 INFO @ Wed, 22 Apr 2020 11:37:49: 18000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:37:56: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:37:56: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:37:56: #1 total tags in treatment: 12156947 INFO @ Wed, 22 Apr 2020 11:37:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:37:56: #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 11:37:56: #1 tags after filtering in treatment: 8552406 INFO @ Wed, 22 Apr 2020 11:37:56: #1 Redundant rate of treatment: 0.30 INFO @ Wed, 22 Apr 2020 11:37:56: #1 finished! INFO @ Wed, 22 Apr 2020 11:37:56: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:37:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:37:57: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:37:57: 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 11:37:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.05_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/SRX7409636/SRX7409636.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:37:58: 19000000 INFO @ Wed, 22 Apr 2020 11:37:58: 23000000 INFO @ Wed, 22 Apr 2020 11:38:07: 20000000 INFO @ Wed, 22 Apr 2020 11:38:07: 24000000 INFO @ Wed, 22 Apr 2020 11:38:16: 21000000 INFO @ Wed, 22 Apr 2020 11:38:16: 25000000 INFO @ Wed, 22 Apr 2020 11:38:25: 22000000 INFO @ Wed, 22 Apr 2020 11:38:26: 26000000 INFO @ Wed, 22 Apr 2020 11:38:34: 23000000 INFO @ Wed, 22 Apr 2020 11:38:35: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:38:35: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:38:35: #1 total tags in treatment: 12156947 INFO @ Wed, 22 Apr 2020 11:38:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:38:35: #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 11:38:35: #1 tags after filtering in treatment: 8552406 INFO @ Wed, 22 Apr 2020 11:38:35: #1 Redundant rate of treatment: 0.30 INFO @ Wed, 22 Apr 2020 11:38:35: #1 finished! INFO @ Wed, 22 Apr 2020 11:38:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:38:36: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:38:36: 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 11:38:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.10_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/SRX7409636/SRX7409636.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:38:42: 24000000 INFO @ Wed, 22 Apr 2020 11:38:50: 25000000 INFO @ Wed, 22 Apr 2020 11:38:59: 26000000 INFO @ Wed, 22 Apr 2020 11:39:07: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:39:07: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:39:07: #1 total tags in treatment: 12156947 INFO @ Wed, 22 Apr 2020 11:39:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:39:07: #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 11:39:08: #1 tags after filtering in treatment: 8552406 INFO @ Wed, 22 Apr 2020 11:39:08: #1 Redundant rate of treatment: 0.30 INFO @ Wed, 22 Apr 2020 11:39:08: #1 finished! INFO @ Wed, 22 Apr 2020 11:39:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:39:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:39:08: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:39:08: 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 11:39:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.20_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/SRX7409636/SRX7409636.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409636/SRX7409636.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling