Job ID = 5791180 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:52:31 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 ) 2020-04-21T23:52:31 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 ) 2020-04-21T23:53:15 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 ) 2020-04-21T23:53:15 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 : 15,215,081 reads read : 30,430,162 reads written : 30,430,162 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: 00:17:44 15215081 reads; of these: 15215081 (100.00%) were paired; of these: 8646083 (56.83%) aligned concordantly 0 times 4858876 (31.93%) aligned concordantly exactly 1 time 1710122 (11.24%) aligned concordantly >1 times ---- 8646083 pairs aligned concordantly 0 times; of these: 3073004 (35.54%) aligned discordantly 1 time ---- 5573079 pairs aligned 0 times concordantly or discordantly; of these: 11146158 mates make up the pairs; of these: 8980205 (80.57%) aligned 0 times 285249 (2.56%) aligned exactly 1 time 1880704 (16.87%) aligned >1 times 70.49% overall alignment rate Time searching: 00:17:44 Overall time: 00:17:44 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] 2188662 / 9467754 = 0.2312 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 09:42:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.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 09:42:51: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:42:51: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:43:00: 1000000 INFO @ Wed, 22 Apr 2020 09:43:08: 2000000 INFO @ Wed, 22 Apr 2020 09:43:17: 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 09:43:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.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 09:43:21: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:43:21: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:43:26: 4000000 INFO @ Wed, 22 Apr 2020 09:43:33: 1000000 INFO @ Wed, 22 Apr 2020 09:43:37: 5000000 INFO @ Wed, 22 Apr 2020 09:43:45: 2000000 INFO @ Wed, 22 Apr 2020 09:43:48: 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 09:43:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.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 09:43:51: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:43:51: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:43:58: 3000000 INFO @ Wed, 22 Apr 2020 09:43:59: 7000000 INFO @ Wed, 22 Apr 2020 09:44:03: 1000000 INFO @ Wed, 22 Apr 2020 09:44:10: 4000000 INFO @ Wed, 22 Apr 2020 09:44:10: 8000000 INFO @ Wed, 22 Apr 2020 09:44:15: 2000000 INFO @ Wed, 22 Apr 2020 09:44:21: 9000000 INFO @ Wed, 22 Apr 2020 09:44:22: 5000000 INFO @ Wed, 22 Apr 2020 09:44:26: 3000000 INFO @ Wed, 22 Apr 2020 09:44:33: 10000000 INFO @ Wed, 22 Apr 2020 09:44:34: 6000000 INFO @ Wed, 22 Apr 2020 09:44:38: 4000000 INFO @ Wed, 22 Apr 2020 09:44:43: 11000000 INFO @ Wed, 22 Apr 2020 09:44:46: 7000000 INFO @ Wed, 22 Apr 2020 09:44:49: 5000000 INFO @ Wed, 22 Apr 2020 09:44:54: 12000000 INFO @ Wed, 22 Apr 2020 09:44:58: 8000000 INFO @ Wed, 22 Apr 2020 09:45:00: 6000000 INFO @ Wed, 22 Apr 2020 09:45:05: 13000000 INFO @ Wed, 22 Apr 2020 09:45:10: 9000000 INFO @ Wed, 22 Apr 2020 09:45:12: 7000000 INFO @ Wed, 22 Apr 2020 09:45:16: 14000000 INFO @ Wed, 22 Apr 2020 09:45:22: 10000000 INFO @ Wed, 22 Apr 2020 09:45:24: 8000000 INFO @ Wed, 22 Apr 2020 09:45:28: 15000000 INFO @ Wed, 22 Apr 2020 09:45:34: 11000000 INFO @ Wed, 22 Apr 2020 09:45:35: 9000000 INFO @ Wed, 22 Apr 2020 09:45:39: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:45:46: 12000000 INFO @ Wed, 22 Apr 2020 09:45:47: 10000000 INFO @ Wed, 22 Apr 2020 09:45:50: 17000000 INFO @ Wed, 22 Apr 2020 09:45:51: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:45:51: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:45:51: #1 total tags in treatment: 4875906 INFO @ Wed, 22 Apr 2020 09:45:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:45:51: #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 09:45:51: #1 tags after filtering in treatment: 3104685 INFO @ Wed, 22 Apr 2020 09:45:51: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 09:45:51: #1 finished! INFO @ Wed, 22 Apr 2020 09:45:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:45:51: #2 number of paired peaks: 23 WARNING @ Wed, 22 Apr 2020 09:45:51: Too few paired peaks (23) 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 09:45:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.05_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/SRX6614972/SRX6614972.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:45:58: 13000000 INFO @ Wed, 22 Apr 2020 09:45:58: 11000000 INFO @ Wed, 22 Apr 2020 09:46:09: 12000000 INFO @ Wed, 22 Apr 2020 09:46:10: 14000000 INFO @ Wed, 22 Apr 2020 09:46:21: 13000000 INFO @ Wed, 22 Apr 2020 09:46:22: 15000000 INFO @ Wed, 22 Apr 2020 09:46:32: 14000000 INFO @ Wed, 22 Apr 2020 09:46:33: 16000000 INFO @ Wed, 22 Apr 2020 09:46:44: 15000000 INFO @ Wed, 22 Apr 2020 09:46:45: 17000000 INFO @ Wed, 22 Apr 2020 09:46:46: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:46:46: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:46:46: #1 total tags in treatment: 4875906 INFO @ Wed, 22 Apr 2020 09:46:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:46:46: #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 09:46:46: #1 tags after filtering in treatment: 3104685 INFO @ Wed, 22 Apr 2020 09:46:46: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 09:46:46: #1 finished! INFO @ Wed, 22 Apr 2020 09:46:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:46:46: #2 number of paired peaks: 23 WARNING @ Wed, 22 Apr 2020 09:46:46: Too few paired peaks (23) 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 09:46:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.10_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/SRX6614972/SRX6614972.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:46:54: 16000000 INFO @ Wed, 22 Apr 2020 09:47:05: 17000000 INFO @ Wed, 22 Apr 2020 09:47:06: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:47:06: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:47:06: #1 total tags in treatment: 4875906 INFO @ Wed, 22 Apr 2020 09:47:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:47:06: #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 09:47:06: #1 tags after filtering in treatment: 3104685 INFO @ Wed, 22 Apr 2020 09:47:06: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 09:47:06: #1 finished! INFO @ Wed, 22 Apr 2020 09:47:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:47:06: #2 number of paired peaks: 23 WARNING @ Wed, 22 Apr 2020 09:47:06: Too few paired peaks (23) 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 09:47:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.20_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/SRX6614972/SRX6614972.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614972/SRX6614972.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling