Job ID = 5791635 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:50:48 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 ) 2020-04-22T00:50:48 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 ) 2020-04-22T00:55:16 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 ) 2020-04-22T00:58:52 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 ) 2020-04-22T00:58:52 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 ) 2020-04-22T00:58:52 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 ) 2020-04-22T00:58:52 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 ) 2020-04-22T01:01:38 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 ) 2020-04-22T01:08:15 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 ) 2020-04-22T01:08:15 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 : 32,778,866 reads read : 65,557,732 reads written : 65,557,732 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: 00:18:07 32778866 reads; of these: 32778866 (100.00%) were paired; of these: 1518715 (4.63%) aligned concordantly 0 times 28373752 (86.56%) aligned concordantly exactly 1 time 2886399 (8.81%) aligned concordantly >1 times ---- 1518715 pairs aligned concordantly 0 times; of these: 56553 (3.72%) aligned discordantly 1 time ---- 1462162 pairs aligned 0 times concordantly or discordantly; of these: 2924324 mates make up the pairs; of these: 2677889 (91.57%) aligned 0 times 200902 (6.87%) aligned exactly 1 time 45533 (1.56%) aligned >1 times 95.92% overall alignment rate Time searching: 00:18:07 Overall time: 00:18:07 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 28 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] 13574256 / 31266818 = 0.4341 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 10:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.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 10:42:14: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:42:14: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:42:18: 1000000 INFO @ Wed, 22 Apr 2020 10:42:23: 2000000 INFO @ Wed, 22 Apr 2020 10:42:28: 3000000 INFO @ Wed, 22 Apr 2020 10:42:33: 4000000 INFO @ Wed, 22 Apr 2020 10:42:38: 5000000 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 10:42:42: 6000000 INFO @ Wed, 22 Apr 2020 10:42:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.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 10:42:44: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:42:44: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:42:48: 7000000 INFO @ Wed, 22 Apr 2020 10:42:50: 1000000 INFO @ Wed, 22 Apr 2020 10:42:53: 8000000 INFO @ Wed, 22 Apr 2020 10:42:57: 2000000 INFO @ Wed, 22 Apr 2020 10:42:59: 9000000 INFO @ Wed, 22 Apr 2020 10:43:03: 3000000 INFO @ Wed, 22 Apr 2020 10:43:04: 10000000 INFO @ Wed, 22 Apr 2020 10:43:10: 4000000 INFO @ Wed, 22 Apr 2020 10:43:10: 11000000 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 10:43:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.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 10:43:14: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:43:14: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:43:16: 12000000 INFO @ Wed, 22 Apr 2020 10:43:16: 5000000 INFO @ Wed, 22 Apr 2020 10:43:20: 1000000 INFO @ Wed, 22 Apr 2020 10:43:21: 13000000 INFO @ Wed, 22 Apr 2020 10:43:22: 6000000 INFO @ Wed, 22 Apr 2020 10:43:26: 2000000 INFO @ Wed, 22 Apr 2020 10:43:27: 14000000 INFO @ Wed, 22 Apr 2020 10:43:29: 7000000 INFO @ Wed, 22 Apr 2020 10:43:32: 15000000 INFO @ Wed, 22 Apr 2020 10:43:33: 3000000 INFO @ Wed, 22 Apr 2020 10:43:35: 8000000 INFO @ Wed, 22 Apr 2020 10:43:38: 16000000 INFO @ Wed, 22 Apr 2020 10:43:39: 4000000 INFO @ Wed, 22 Apr 2020 10:43:41: 9000000 INFO @ Wed, 22 Apr 2020 10:43:43: 17000000 INFO @ Wed, 22 Apr 2020 10:43:45: 5000000 INFO @ Wed, 22 Apr 2020 10:43:47: 10000000 INFO @ Wed, 22 Apr 2020 10:43:49: 18000000 INFO @ Wed, 22 Apr 2020 10:43:52: 6000000 INFO @ Wed, 22 Apr 2020 10:43:53: 11000000 INFO @ Wed, 22 Apr 2020 10:43:54: 19000000 INFO @ Wed, 22 Apr 2020 10:43:58: 7000000 INFO @ Wed, 22 Apr 2020 10:43:59: 12000000 INFO @ Wed, 22 Apr 2020 10:44:00: 20000000 INFO @ Wed, 22 Apr 2020 10:44:04: 8000000 INFO @ Wed, 22 Apr 2020 10:44:05: 21000000 INFO @ Wed, 22 Apr 2020 10:44:06: 13000000 INFO @ Wed, 22 Apr 2020 10:44:10: 9000000 INFO @ Wed, 22 Apr 2020 10:44:11: 22000000 INFO @ Wed, 22 Apr 2020 10:44:12: 14000000 INFO @ Wed, 22 Apr 2020 10:44:16: 23000000 INFO @ Wed, 22 Apr 2020 10:44:17: 10000000 INFO @ Wed, 22 Apr 2020 10:44:18: 15000000 INFO @ Wed, 22 Apr 2020 10:44:22: 24000000 INFO @ Wed, 22 Apr 2020 10:44:23: 11000000 INFO @ Wed, 22 Apr 2020 10:44:25: 16000000 INFO @ Wed, 22 Apr 2020 10:44:27: 25000000 INFO @ Wed, 22 Apr 2020 10:44:29: 12000000 INFO @ Wed, 22 Apr 2020 10:44:31: 17000000 INFO @ Wed, 22 Apr 2020 10:44:33: 26000000 INFO @ Wed, 22 Apr 2020 10:44:35: 13000000 INFO @ Wed, 22 Apr 2020 10:44:37: 18000000 INFO @ Wed, 22 Apr 2020 10:44:38: 27000000 INFO @ Wed, 22 Apr 2020 10:44:41: 14000000 INFO @ Wed, 22 Apr 2020 10:44:43: 19000000 INFO @ Wed, 22 Apr 2020 10:44:44: 28000000 INFO @ Wed, 22 Apr 2020 10:44:48: 15000000 INFO @ Wed, 22 Apr 2020 10:44:49: 29000000 INFO @ Wed, 22 Apr 2020 10:44:50: 20000000 INFO @ Wed, 22 Apr 2020 10:44:54: 16000000 INFO @ Wed, 22 Apr 2020 10:44:55: 30000000 INFO @ Wed, 22 Apr 2020 10:44:56: 21000000 INFO @ Wed, 22 Apr 2020 10:45:00: 17000000 INFO @ Wed, 22 Apr 2020 10:45:01: 31000000 INFO @ Wed, 22 Apr 2020 10:45:02: 22000000 INFO @ Wed, 22 Apr 2020 10:45:06: 32000000 INFO @ Wed, 22 Apr 2020 10:45:07: 18000000 INFO @ Wed, 22 Apr 2020 10:45:08: 23000000 INFO @ Wed, 22 Apr 2020 10:45:11: 33000000 INFO @ Wed, 22 Apr 2020 10:45:13: 19000000 INFO @ Wed, 22 Apr 2020 10:45:15: 24000000 INFO @ Wed, 22 Apr 2020 10:45:17: 34000000 INFO @ Wed, 22 Apr 2020 10:45:19: 20000000 INFO @ Wed, 22 Apr 2020 10:45:21: 25000000 INFO @ Wed, 22 Apr 2020 10:45:22: 35000000 INFO @ Wed, 22 Apr 2020 10:45:25: 21000000 INFO @ Wed, 22 Apr 2020 10:45:27: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:45:27: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:45:27: #1 total tags in treatment: 17688547 INFO @ Wed, 22 Apr 2020 10:45:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:45:27: #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 10:45:27: #1 tags after filtering in treatment: 9874438 INFO @ Wed, 22 Apr 2020 10:45:27: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 22 Apr 2020 10:45:27: #1 finished! INFO @ Wed, 22 Apr 2020 10:45:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:45:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:45:27: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:45:27: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:45:27: 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 10:45:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.05_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/SRX7409602/SRX7409602.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:45:32: 22000000 INFO @ Wed, 22 Apr 2020 10:45:33: 27000000 INFO @ Wed, 22 Apr 2020 10:45:38: 23000000 INFO @ Wed, 22 Apr 2020 10:45:39: 28000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:45:44: 24000000 INFO @ Wed, 22 Apr 2020 10:45:45: 29000000 INFO @ Wed, 22 Apr 2020 10:45:50: 25000000 INFO @ Wed, 22 Apr 2020 10:45:51: 30000000 INFO @ Wed, 22 Apr 2020 10:45:56: 26000000 INFO @ Wed, 22 Apr 2020 10:45:57: 31000000 INFO @ Wed, 22 Apr 2020 10:46:02: 32000000 INFO @ Wed, 22 Apr 2020 10:46:03: 27000000 INFO @ Wed, 22 Apr 2020 10:46:08: 33000000 INFO @ Wed, 22 Apr 2020 10:46:09: 28000000 INFO @ Wed, 22 Apr 2020 10:46:14: 34000000 INFO @ Wed, 22 Apr 2020 10:46:15: 29000000 INFO @ Wed, 22 Apr 2020 10:46:20: 35000000 INFO @ Wed, 22 Apr 2020 10:46:20: 30000000 INFO @ Wed, 22 Apr 2020 10:46:24: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:46:24: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:46:24: #1 total tags in treatment: 17688547 INFO @ Wed, 22 Apr 2020 10:46:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:46:24: #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 10:46:25: #1 tags after filtering in treatment: 9874438 INFO @ Wed, 22 Apr 2020 10:46:25: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 22 Apr 2020 10:46:25: #1 finished! INFO @ Wed, 22 Apr 2020 10:46:25: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:46:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:46:25: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:46:25: 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 10:46:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.10_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/SRX7409602/SRX7409602.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:46:26: 31000000 INFO @ Wed, 22 Apr 2020 10:46:32: 32000000 INFO @ Wed, 22 Apr 2020 10:46:38: 33000000 INFO @ Wed, 22 Apr 2020 10:46:43: 34000000 INFO @ Wed, 22 Apr 2020 10:46:49: 35000000 INFO @ Wed, 22 Apr 2020 10:46:53: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:46:53: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:46:53: #1 total tags in treatment: 17688547 INFO @ Wed, 22 Apr 2020 10:46:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:46:53: #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 10:46:54: #1 tags after filtering in treatment: 9874438 INFO @ Wed, 22 Apr 2020 10:46:54: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 22 Apr 2020 10:46:54: #1 finished! INFO @ Wed, 22 Apr 2020 10:46:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:46:54: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:46:54: 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 10:46:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.20_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/SRX7409602/SRX7409602.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409602/SRX7409602.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling