Job ID = 5791173 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:54:45 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 ) 2020-04-21T23:54:45 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 ) 2020-04-22T00:01:26 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 ) 2020-04-22T00:01:26 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 ) 2020-04-22T00:01:26 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 ) 2020-04-22T00:01:26 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 : 14,106,929 reads read : 28,213,858 reads written : 28,213,858 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: 00:17:45 14106929 reads; of these: 14106929 (100.00%) were paired; of these: 8619065 (61.10%) aligned concordantly 0 times 4530456 (32.12%) aligned concordantly exactly 1 time 957408 (6.79%) aligned concordantly >1 times ---- 8619065 pairs aligned concordantly 0 times; of these: 4185052 (48.56%) aligned discordantly 1 time ---- 4434013 pairs aligned 0 times concordantly or discordantly; of these: 8868026 mates make up the pairs; of these: 7189010 (81.07%) aligned 0 times 361949 (4.08%) aligned exactly 1 time 1317067 (14.85%) aligned >1 times 74.52% overall alignment rate Time searching: 00:17:45 Overall time: 00:17:45 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] 1714472 / 9482509 = 0.1808 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 09:37:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.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 09:37:12: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:37:12: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:37:20: 1000000 INFO @ Wed, 22 Apr 2020 09:37:29: 2000000 INFO @ Wed, 22 Apr 2020 09:37:38: 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 09:37:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.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 09:37:42: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:37:42: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:37:48: 4000000 INFO @ Wed, 22 Apr 2020 09:37:51: 1000000 INFO @ Wed, 22 Apr 2020 09:37:58: 5000000 INFO @ Wed, 22 Apr 2020 09:38:01: 2000000 INFO @ Wed, 22 Apr 2020 09:38:09: 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 09:38:10: 3000000 INFO @ Wed, 22 Apr 2020 09:38:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.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 09:38:12: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:38:12: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:38:19: 7000000 INFO @ Wed, 22 Apr 2020 09:38:19: 4000000 INFO @ Wed, 22 Apr 2020 09:38:22: 1000000 INFO @ Wed, 22 Apr 2020 09:38:29: 5000000 INFO @ Wed, 22 Apr 2020 09:38:30: 8000000 INFO @ Wed, 22 Apr 2020 09:38:31: 2000000 INFO @ Wed, 22 Apr 2020 09:38:38: 6000000 INFO @ Wed, 22 Apr 2020 09:38:40: 9000000 INFO @ Wed, 22 Apr 2020 09:38:41: 3000000 INFO @ Wed, 22 Apr 2020 09:38:47: 7000000 INFO @ Wed, 22 Apr 2020 09:38:51: 10000000 INFO @ Wed, 22 Apr 2020 09:38:51: 4000000 INFO @ Wed, 22 Apr 2020 09:38:56: 8000000 INFO @ Wed, 22 Apr 2020 09:39:00: 5000000 INFO @ Wed, 22 Apr 2020 09:39:01: 11000000 INFO @ Wed, 22 Apr 2020 09:39:05: 9000000 INFO @ Wed, 22 Apr 2020 09:39:09: 6000000 INFO @ Wed, 22 Apr 2020 09:39:11: 12000000 INFO @ Wed, 22 Apr 2020 09:39:14: 10000000 INFO @ Wed, 22 Apr 2020 09:39:19: 7000000 INFO @ Wed, 22 Apr 2020 09:39:21: 13000000 INFO @ Wed, 22 Apr 2020 09:39:24: 11000000 INFO @ Wed, 22 Apr 2020 09:39:28: 8000000 INFO @ Wed, 22 Apr 2020 09:39:31: 14000000 INFO @ Wed, 22 Apr 2020 09:39:33: 12000000 INFO @ Wed, 22 Apr 2020 09:39:37: 9000000 INFO @ Wed, 22 Apr 2020 09:39:42: 15000000 INFO @ Wed, 22 Apr 2020 09:39:42: 13000000 INFO @ Wed, 22 Apr 2020 09:39:47: 10000000 INFO @ Wed, 22 Apr 2020 09:39:51: 14000000 INFO @ Wed, 22 Apr 2020 09:39:52: 16000000 INFO @ Wed, 22 Apr 2020 09:39:56: 11000000 INFO @ Wed, 22 Apr 2020 09:40:00: 15000000 INFO @ Wed, 22 Apr 2020 09:40:02: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:40:05: 12000000 INFO @ Wed, 22 Apr 2020 09:40:08: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:40:08: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:40:08: #1 total tags in treatment: 4489393 INFO @ Wed, 22 Apr 2020 09:40:08: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:40:08: #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 09:40:09: #1 tags after filtering in treatment: 2957323 INFO @ Wed, 22 Apr 2020 09:40:09: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Apr 2020 09:40:09: #1 finished! INFO @ Wed, 22 Apr 2020 09:40:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:40:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:40:09: #2 number of paired peaks: 6 WARNING @ Wed, 22 Apr 2020 09:40:09: Too few paired peaks (6) 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 09:40:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.05_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/SRX6614966/SRX6614966.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:40:09: 16000000 INFO @ Wed, 22 Apr 2020 09:40:14: 13000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:40:18: 17000000 INFO @ Wed, 22 Apr 2020 09:40:23: 14000000 INFO @ Wed, 22 Apr 2020 09:40:23: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:40:23: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:40:23: #1 total tags in treatment: 4489393 INFO @ Wed, 22 Apr 2020 09:40:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:40:23: #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 09:40:24: #1 tags after filtering in treatment: 2957323 INFO @ Wed, 22 Apr 2020 09:40:24: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Apr 2020 09:40:24: #1 finished! INFO @ Wed, 22 Apr 2020 09:40:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:40:24: #2 number of paired peaks: 6 WARNING @ Wed, 22 Apr 2020 09:40:24: Too few paired peaks (6) 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 09:40:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.10_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/SRX6614966/SRX6614966.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:40:32: 15000000 INFO @ Wed, 22 Apr 2020 09:40:40: 16000000 INFO @ Wed, 22 Apr 2020 09:40:48: 17000000 INFO @ Wed, 22 Apr 2020 09:40:53: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:40:53: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:40:53: #1 total tags in treatment: 4489393 INFO @ Wed, 22 Apr 2020 09:40:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:40:53: #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 09:40:53: #1 tags after filtering in treatment: 2957323 INFO @ Wed, 22 Apr 2020 09:40:53: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Apr 2020 09:40:53: #1 finished! INFO @ Wed, 22 Apr 2020 09:40:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:40:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:40:53: #2 number of paired peaks: 6 WARNING @ Wed, 22 Apr 2020 09:40:53: Too few paired peaks (6) 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 09:40:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614966/SRX6614966.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling