Job ID = 5791115 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:32:08 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 ) 2020-04-21T23:34:04 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 ) 2020-04-21T23:34:04 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 ) 2020-04-21T23:35:06 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 ) 2020-04-21T23:36:09 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 ) 2020-04-21T23:43:28 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 ) 2020-04-21T23:43:55 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 : 20,751,458 reads read : 41,502,916 reads written : 41,502,916 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: 00:09:18 20751458 reads; of these: 20751458 (100.00%) were paired; of these: 4044727 (19.49%) aligned concordantly 0 times 14361059 (69.21%) aligned concordantly exactly 1 time 2345672 (11.30%) aligned concordantly >1 times ---- 4044727 pairs aligned concordantly 0 times; of these: 448553 (11.09%) aligned discordantly 1 time ---- 3596174 pairs aligned 0 times concordantly or discordantly; of these: 7192348 mates make up the pairs; of these: 6460028 (89.82%) aligned 0 times 386113 (5.37%) aligned exactly 1 time 346207 (4.81%) aligned >1 times 84.43% overall alignment rate Time searching: 00:09:18 Overall time: 00:09:18 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 16 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] 2096731 / 17127312 = 0.1224 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 09:04:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.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 09:04:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:04:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:04:54: 1000000 INFO @ Wed, 22 Apr 2020 09:04:58: 2000000 INFO @ Wed, 22 Apr 2020 09:05:02: 3000000 INFO @ Wed, 22 Apr 2020 09:05:06: 4000000 INFO @ Wed, 22 Apr 2020 09:05:11: 5000000 INFO @ Wed, 22 Apr 2020 09:05:15: 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 09:05:19: 7000000 INFO @ Wed, 22 Apr 2020 09:05:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.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 09:05:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:05:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:05:23: 8000000 INFO @ Wed, 22 Apr 2020 09:05:24: 1000000 INFO @ Wed, 22 Apr 2020 09:05:28: 9000000 INFO @ Wed, 22 Apr 2020 09:05:28: 2000000 INFO @ Wed, 22 Apr 2020 09:05:32: 10000000 INFO @ Wed, 22 Apr 2020 09:05:32: 3000000 INFO @ Wed, 22 Apr 2020 09:05:36: 11000000 INFO @ Wed, 22 Apr 2020 09:05:37: 4000000 INFO @ Wed, 22 Apr 2020 09:05:40: 12000000 INFO @ Wed, 22 Apr 2020 09:05:41: 5000000 INFO @ Wed, 22 Apr 2020 09:05:44: 13000000 INFO @ Wed, 22 Apr 2020 09:05:45: 6000000 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 09:05:49: 14000000 INFO @ Wed, 22 Apr 2020 09:05:49: 7000000 INFO @ Wed, 22 Apr 2020 09:05:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.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 09:05:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:05:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:05:53: 15000000 INFO @ Wed, 22 Apr 2020 09:05:54: 8000000 INFO @ Wed, 22 Apr 2020 09:05:55: 1000000 INFO @ Wed, 22 Apr 2020 09:05:57: 16000000 INFO @ Wed, 22 Apr 2020 09:05:58: 9000000 INFO @ Wed, 22 Apr 2020 09:06:00: 2000000 INFO @ Wed, 22 Apr 2020 09:06:02: 17000000 INFO @ Wed, 22 Apr 2020 09:06:02: 10000000 INFO @ Wed, 22 Apr 2020 09:06:05: 3000000 INFO @ Wed, 22 Apr 2020 09:06:06: 18000000 INFO @ Wed, 22 Apr 2020 09:06:06: 11000000 INFO @ Wed, 22 Apr 2020 09:06:09: 4000000 INFO @ Wed, 22 Apr 2020 09:06:10: 19000000 INFO @ Wed, 22 Apr 2020 09:06:11: 12000000 INFO @ Wed, 22 Apr 2020 09:06:14: 20000000 INFO @ Wed, 22 Apr 2020 09:06:14: 5000000 INFO @ Wed, 22 Apr 2020 09:06:15: 13000000 INFO @ Wed, 22 Apr 2020 09:06:18: 21000000 INFO @ Wed, 22 Apr 2020 09:06:19: 6000000 INFO @ Wed, 22 Apr 2020 09:06:20: 14000000 INFO @ Wed, 22 Apr 2020 09:06:23: 22000000 INFO @ Wed, 22 Apr 2020 09:06:24: 15000000 INFO @ Wed, 22 Apr 2020 09:06:24: 7000000 INFO @ Wed, 22 Apr 2020 09:06:27: 23000000 INFO @ Wed, 22 Apr 2020 09:06:28: 16000000 INFO @ Wed, 22 Apr 2020 09:06:29: 8000000 INFO @ Wed, 22 Apr 2020 09:06:32: 24000000 INFO @ Wed, 22 Apr 2020 09:06:32: 17000000 INFO @ Wed, 22 Apr 2020 09:06:34: 9000000 INFO @ Wed, 22 Apr 2020 09:06:36: 25000000 INFO @ Wed, 22 Apr 2020 09:06:37: 18000000 INFO @ Wed, 22 Apr 2020 09:06:39: 10000000 INFO @ Wed, 22 Apr 2020 09:06:40: 26000000 INFO @ Wed, 22 Apr 2020 09:06:41: 19000000 INFO @ Wed, 22 Apr 2020 09:06:44: 11000000 INFO @ Wed, 22 Apr 2020 09:06:44: 27000000 INFO @ Wed, 22 Apr 2020 09:06:45: 20000000 INFO @ Wed, 22 Apr 2020 09:06:49: 28000000 INFO @ Wed, 22 Apr 2020 09:06:49: 21000000 INFO @ Wed, 22 Apr 2020 09:06:49: 12000000 INFO @ Wed, 22 Apr 2020 09:06:53: 29000000 INFO @ Wed, 22 Apr 2020 09:06:53: 22000000 INFO @ Wed, 22 Apr 2020 09:06:54: 13000000 INFO @ Wed, 22 Apr 2020 09:06:57: 30000000 INFO @ Wed, 22 Apr 2020 09:06:58: 23000000 INFO @ Wed, 22 Apr 2020 09:06:59: 14000000 INFO @ Wed, 22 Apr 2020 09:07:01: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 09:07:01: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 09:07:01: #1 total tags in treatment: 14631707 INFO @ Wed, 22 Apr 2020 09:07:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:07:01: #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 09:07:01: #1 tags after filtering in treatment: 9871622 INFO @ Wed, 22 Apr 2020 09:07:01: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 09:07:01: #1 finished! INFO @ Wed, 22 Apr 2020 09:07:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:07:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:07:02: 24000000 INFO @ Wed, 22 Apr 2020 09:07:02: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:07:02: 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 09:07:02: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 09:07:04: 15000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.05_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/SRX6078426/SRX6078426.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:07:06: 25000000 INFO @ Wed, 22 Apr 2020 09:07:09: 16000000 INFO @ Wed, 22 Apr 2020 09:07:11: 26000000 INFO @ Wed, 22 Apr 2020 09:07:14: 17000000 INFO @ Wed, 22 Apr 2020 09:07:15: 27000000 INFO @ Wed, 22 Apr 2020 09:07:18: 18000000 INFO @ Wed, 22 Apr 2020 09:07:19: 28000000 INFO @ Wed, 22 Apr 2020 09:07:23: 19000000 INFO @ Wed, 22 Apr 2020 09:07:23: 29000000 INFO @ Wed, 22 Apr 2020 09:07:27: 30000000 INFO @ Wed, 22 Apr 2020 09:07:28: 20000000 INFO @ Wed, 22 Apr 2020 09:07:31: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 09:07:31: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 09:07:31: #1 total tags in treatment: 14631707 INFO @ Wed, 22 Apr 2020 09:07:31: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:07:31: #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 09:07:31: #1 tags after filtering in treatment: 9871622 INFO @ Wed, 22 Apr 2020 09:07:31: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 09:07:31: #1 finished! INFO @ Wed, 22 Apr 2020 09:07:31: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:07:32: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:07:32: 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 09:07:32: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 09:07:32: 21000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.10_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/SRX6078426/SRX6078426.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:07:37: 22000000 INFO @ Wed, 22 Apr 2020 09:07:42: 23000000 INFO @ Wed, 22 Apr 2020 09:07:47: 24000000 INFO @ Wed, 22 Apr 2020 09:07:52: 25000000 INFO @ Wed, 22 Apr 2020 09:07:57: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:08:02: 27000000 INFO @ Wed, 22 Apr 2020 09:08:07: 28000000 INFO @ Wed, 22 Apr 2020 09:08:12: 29000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:08:17: 30000000 INFO @ Wed, 22 Apr 2020 09:08:21: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 09:08:21: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 09:08:21: #1 total tags in treatment: 14631707 INFO @ Wed, 22 Apr 2020 09:08:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:08:21: #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 09:08:22: #1 tags after filtering in treatment: 9871622 INFO @ Wed, 22 Apr 2020 09:08:22: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 09:08:22: #1 finished! INFO @ Wed, 22 Apr 2020 09:08:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:08:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:08:22: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:08:22: 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 09:08:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.20_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/SRX6078426/SRX6078426.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6078426/SRX6078426.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling