Job ID = 5791148 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:37:41 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 ) 2020-04-21T23:37:41 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 ) 2020-04-21T23:42:39 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 ) 2020-04-21T23:49:45 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 ) 2020-04-21T23:53:05 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 ) 2020-04-21T23:55:06 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 ) 2020-04-21T23:55:11 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 ) 2020-04-22T00:10:03 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 : 14,331,050 reads read : 28,662,100 reads written : 28,662,100 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: 00:19:30 14331050 reads; of these: 14331050 (100.00%) were paired; of these: 8217783 (57.34%) aligned concordantly 0 times 3813402 (26.61%) aligned concordantly exactly 1 time 2299865 (16.05%) aligned concordantly >1 times ---- 8217783 pairs aligned concordantly 0 times; of these: 3298032 (40.13%) aligned discordantly 1 time ---- 4919751 pairs aligned 0 times concordantly or discordantly; of these: 9839502 mates make up the pairs; of these: 6676158 (67.85%) aligned 0 times 378665 (3.85%) aligned exactly 1 time 2784679 (28.30%) aligned >1 times 76.71% overall alignment rate Time searching: 00:19:30 Overall time: 00:19:30 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] 2618074 / 9210938 = 0.2842 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 09:40:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.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 09:40:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:40:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:41:10: 1000000 INFO @ Wed, 22 Apr 2020 09:41:19: 2000000 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 09:41:29: 3000000 INFO @ Wed, 22 Apr 2020 09:41:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.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 09:41:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:41:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:41:39: 1000000 INFO @ Wed, 22 Apr 2020 09:41:40: 4000000 INFO @ Wed, 22 Apr 2020 09:41:49: 2000000 INFO @ Wed, 22 Apr 2020 09:41:50: 5000000 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 09:41:58: 3000000 INFO @ Wed, 22 Apr 2020 09:42:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.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 09:42:00: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:42:00: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:42:01: 6000000 INFO @ Wed, 22 Apr 2020 09:42:08: 4000000 INFO @ Wed, 22 Apr 2020 09:42:11: 1000000 INFO @ Wed, 22 Apr 2020 09:42:12: 7000000 INFO @ Wed, 22 Apr 2020 09:42:18: 5000000 INFO @ Wed, 22 Apr 2020 09:42:22: 2000000 INFO @ Wed, 22 Apr 2020 09:42:23: 8000000 INFO @ Wed, 22 Apr 2020 09:42:27: 6000000 INFO @ Wed, 22 Apr 2020 09:42:33: 3000000 INFO @ Wed, 22 Apr 2020 09:42:34: 9000000 INFO @ Wed, 22 Apr 2020 09:42:37: 7000000 INFO @ Wed, 22 Apr 2020 09:42:46: 8000000 INFO @ Wed, 22 Apr 2020 09:42:49: 4000000 INFO @ Wed, 22 Apr 2020 09:42:51: 10000000 INFO @ Wed, 22 Apr 2020 09:42:56: 9000000 INFO @ Wed, 22 Apr 2020 09:43:05: 10000000 INFO @ Wed, 22 Apr 2020 09:43:06: 5000000 INFO @ Wed, 22 Apr 2020 09:43:08: 11000000 INFO @ Wed, 22 Apr 2020 09:43:14: 11000000 INFO @ Wed, 22 Apr 2020 09:43:23: 12000000 INFO @ Wed, 22 Apr 2020 09:43:23: 12000000 INFO @ Wed, 22 Apr 2020 09:43:24: 6000000 INFO @ Wed, 22 Apr 2020 09:43:33: 13000000 INFO @ Wed, 22 Apr 2020 09:43:40: 13000000 INFO @ Wed, 22 Apr 2020 09:43:41: 7000000 INFO @ Wed, 22 Apr 2020 09:43:42: 14000000 INFO @ Wed, 22 Apr 2020 09:43:52: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:43:53: 14000000 INFO @ Wed, 22 Apr 2020 09:43:55: 8000000 INFO @ Wed, 22 Apr 2020 09:44:01: 16000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:44:04: 15000000 INFO @ Wed, 22 Apr 2020 09:44:06: 9000000 INFO @ Wed, 22 Apr 2020 09:44:08: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:44:08: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:44:08: #1 total tags in treatment: 4131868 INFO @ Wed, 22 Apr 2020 09:44:08: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:44:08: #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 09:44:08: #1 tags after filtering in treatment: 2522604 INFO @ Wed, 22 Apr 2020 09:44:08: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 22 Apr 2020 09:44:08: #1 finished! INFO @ Wed, 22 Apr 2020 09:44:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:44:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:44:09: #2 number of paired peaks: 35 WARNING @ Wed, 22 Apr 2020 09:44:09: Too few paired peaks (35) 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 09:44:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.10_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/SRX6614941/SRX6614941.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:44:14: 16000000 INFO @ Wed, 22 Apr 2020 09:44:17: 10000000 INFO @ Wed, 22 Apr 2020 09:44:22: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:44:22: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:44:22: #1 total tags in treatment: 4131868 INFO @ Wed, 22 Apr 2020 09:44:22: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:44:22: #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 09:44:22: #1 tags after filtering in treatment: 2522604 INFO @ Wed, 22 Apr 2020 09:44:22: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 22 Apr 2020 09:44:22: #1 finished! INFO @ Wed, 22 Apr 2020 09:44:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:44:23: #2 number of paired peaks: 35 WARNING @ Wed, 22 Apr 2020 09:44:23: Too few paired peaks (35) 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 09:44:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.05_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/SRX6614941/SRX6614941.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:44:28: 11000000 INFO @ Wed, 22 Apr 2020 09:44:38: 12000000 INFO @ Wed, 22 Apr 2020 09:44:47: 13000000 INFO @ Wed, 22 Apr 2020 09:44:57: 14000000 INFO @ Wed, 22 Apr 2020 09:45:07: 15000000 INFO @ Wed, 22 Apr 2020 09:45:17: 16000000 INFO @ Wed, 22 Apr 2020 09:45:24: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:45:24: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:45:24: #1 total tags in treatment: 4131868 INFO @ Wed, 22 Apr 2020 09:45:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:45:24: #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 09:45:24: #1 tags after filtering in treatment: 2522604 INFO @ Wed, 22 Apr 2020 09:45:24: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 22 Apr 2020 09:45:24: #1 finished! INFO @ Wed, 22 Apr 2020 09:45:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:45:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:45:24: #2 number of paired peaks: 35 WARNING @ Wed, 22 Apr 2020 09:45:24: Too few paired peaks (35) 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 09:45:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.20_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/SRX6614941/SRX6614941.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614941/SRX6614941.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling