Job ID = 5791494 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:41:56 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 ) 2020-04-22T00:43:56 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 ) 2020-04-22T00:52:06 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 ) spots read : 28,657,188 reads read : 57,314,376 reads written : 57,314,376 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: 00:17:58 28657188 reads; of these: 28657188 (100.00%) were paired; of these: 361278 (1.26%) aligned concordantly 0 times 25400532 (88.64%) aligned concordantly exactly 1 time 2895378 (10.10%) aligned concordantly >1 times ---- 361278 pairs aligned concordantly 0 times; of these: 103642 (28.69%) aligned discordantly 1 time ---- 257636 pairs aligned 0 times concordantly or discordantly; of these: 515272 mates make up the pairs; of these: 306434 (59.47%) aligned 0 times 153969 (29.88%) aligned exactly 1 time 54869 (10.65%) aligned >1 times 99.47% overall alignment rate Time searching: 00:17:58 Overall time: 00:17:58 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 24 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] 5449993 / 28308476 = 0.1925 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 10:49:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.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 10:49:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:49:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:49:06: 1000000 INFO @ Wed, 22 Apr 2020 10:49:11: 2000000 INFO @ Wed, 22 Apr 2020 10:49:16: 3000000 INFO @ Wed, 22 Apr 2020 10:49:21: 4000000 INFO @ Wed, 22 Apr 2020 10:49:26: 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 10:49:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.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 10:49:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:49:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:49:31: 6000000 INFO @ Wed, 22 Apr 2020 10:49:36: 1000000 INFO @ Wed, 22 Apr 2020 10:49:37: 7000000 INFO @ Wed, 22 Apr 2020 10:49:42: 2000000 INFO @ Wed, 22 Apr 2020 10:49:42: 8000000 INFO @ Wed, 22 Apr 2020 10:49:47: 3000000 INFO @ Wed, 22 Apr 2020 10:49:48: 9000000 INFO @ Wed, 22 Apr 2020 10:49:53: 4000000 INFO @ Wed, 22 Apr 2020 10:49:53: 10000000 INFO @ Wed, 22 Apr 2020 10:49:58: 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 10:49:59: 11000000 INFO @ Wed, 22 Apr 2020 10:50:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.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 10:50:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:50:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:50:04: 6000000 INFO @ Wed, 22 Apr 2020 10:50:05: 12000000 INFO @ Wed, 22 Apr 2020 10:50:07: 1000000 INFO @ Wed, 22 Apr 2020 10:50:10: 7000000 INFO @ Wed, 22 Apr 2020 10:50:11: 13000000 INFO @ Wed, 22 Apr 2020 10:50:13: 2000000 INFO @ Wed, 22 Apr 2020 10:50:16: 8000000 INFO @ Wed, 22 Apr 2020 10:50:16: 14000000 INFO @ Wed, 22 Apr 2020 10:50:19: 3000000 INFO @ Wed, 22 Apr 2020 10:50:22: 9000000 INFO @ Wed, 22 Apr 2020 10:50:22: 15000000 INFO @ Wed, 22 Apr 2020 10:50:25: 4000000 INFO @ Wed, 22 Apr 2020 10:50:27: 10000000 INFO @ Wed, 22 Apr 2020 10:50:28: 16000000 INFO @ Wed, 22 Apr 2020 10:50:31: 5000000 INFO @ Wed, 22 Apr 2020 10:50:33: 11000000 INFO @ Wed, 22 Apr 2020 10:50:33: 17000000 INFO @ Wed, 22 Apr 2020 10:50:36: 6000000 INFO @ Wed, 22 Apr 2020 10:50:39: 12000000 INFO @ Wed, 22 Apr 2020 10:50:39: 18000000 INFO @ Wed, 22 Apr 2020 10:50:42: 7000000 INFO @ Wed, 22 Apr 2020 10:50:44: 13000000 INFO @ Wed, 22 Apr 2020 10:50:45: 19000000 INFO @ Wed, 22 Apr 2020 10:50:47: 8000000 INFO @ Wed, 22 Apr 2020 10:50:50: 14000000 INFO @ Wed, 22 Apr 2020 10:50:50: 20000000 INFO @ Wed, 22 Apr 2020 10:50:53: 9000000 INFO @ Wed, 22 Apr 2020 10:50:56: 15000000 INFO @ Wed, 22 Apr 2020 10:50:56: 21000000 INFO @ Wed, 22 Apr 2020 10:50:58: 10000000 INFO @ Wed, 22 Apr 2020 10:51:01: 22000000 INFO @ Wed, 22 Apr 2020 10:51:01: 16000000 INFO @ Wed, 22 Apr 2020 10:51:04: 11000000 INFO @ Wed, 22 Apr 2020 10:51:06: 23000000 INFO @ Wed, 22 Apr 2020 10:51:07: 17000000 INFO @ Wed, 22 Apr 2020 10:51:09: 12000000 INFO @ Wed, 22 Apr 2020 10:51:12: 24000000 INFO @ Wed, 22 Apr 2020 10:51:12: 18000000 INFO @ Wed, 22 Apr 2020 10:51:14: 13000000 INFO @ Wed, 22 Apr 2020 10:51:17: 25000000 INFO @ Wed, 22 Apr 2020 10:51:17: 19000000 INFO @ Wed, 22 Apr 2020 10:51:19: 14000000 INFO @ Wed, 22 Apr 2020 10:51:22: 26000000 INFO @ Wed, 22 Apr 2020 10:51:22: 20000000 INFO @ Wed, 22 Apr 2020 10:51:25: 15000000 INFO @ Wed, 22 Apr 2020 10:51:28: 27000000 INFO @ Wed, 22 Apr 2020 10:51:28: 21000000 INFO @ Wed, 22 Apr 2020 10:51:30: 16000000 INFO @ Wed, 22 Apr 2020 10:51:33: 28000000 INFO @ Wed, 22 Apr 2020 10:51:33: 22000000 INFO @ Wed, 22 Apr 2020 10:51:35: 17000000 INFO @ Wed, 22 Apr 2020 10:51:38: 29000000 INFO @ Wed, 22 Apr 2020 10:51:38: 23000000 INFO @ Wed, 22 Apr 2020 10:51:40: 18000000 INFO @ Wed, 22 Apr 2020 10:51:43: 24000000 INFO @ Wed, 22 Apr 2020 10:51:44: 30000000 INFO @ Wed, 22 Apr 2020 10:51:45: 19000000 INFO @ Wed, 22 Apr 2020 10:51:49: 25000000 INFO @ Wed, 22 Apr 2020 10:51:49: 31000000 INFO @ Wed, 22 Apr 2020 10:51:51: 20000000 INFO @ Wed, 22 Apr 2020 10:51:54: 26000000 INFO @ Wed, 22 Apr 2020 10:51:54: 32000000 INFO @ Wed, 22 Apr 2020 10:51:56: 21000000 INFO @ Wed, 22 Apr 2020 10:52:00: 27000000 INFO @ Wed, 22 Apr 2020 10:52:00: 33000000 INFO @ Wed, 22 Apr 2020 10:52:02: 22000000 INFO @ Wed, 22 Apr 2020 10:52:05: 28000000 INFO @ Wed, 22 Apr 2020 10:52:06: 34000000 INFO @ Wed, 22 Apr 2020 10:52:07: 23000000 INFO @ Wed, 22 Apr 2020 10:52:11: 29000000 INFO @ Wed, 22 Apr 2020 10:52:11: 35000000 INFO @ Wed, 22 Apr 2020 10:52:13: 24000000 INFO @ Wed, 22 Apr 2020 10:52:16: 30000000 INFO @ Wed, 22 Apr 2020 10:52:17: 36000000 INFO @ Wed, 22 Apr 2020 10:52:18: 25000000 INFO @ Wed, 22 Apr 2020 10:52:22: 31000000 INFO @ Wed, 22 Apr 2020 10:52:22: 37000000 INFO @ Wed, 22 Apr 2020 10:52:24: 26000000 INFO @ Wed, 22 Apr 2020 10:52:27: 32000000 INFO @ Wed, 22 Apr 2020 10:52:28: 38000000 INFO @ Wed, 22 Apr 2020 10:52:29: 27000000 INFO @ Wed, 22 Apr 2020 10:52:33: 33000000 INFO @ Wed, 22 Apr 2020 10:52:34: 39000000 INFO @ Wed, 22 Apr 2020 10:52:35: 28000000 INFO @ Wed, 22 Apr 2020 10:52:38: 34000000 INFO @ Wed, 22 Apr 2020 10:52:39: 40000000 INFO @ Wed, 22 Apr 2020 10:52:41: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:52:44: 35000000 INFO @ Wed, 22 Apr 2020 10:52:45: 41000000 INFO @ Wed, 22 Apr 2020 10:52:46: 30000000 INFO @ Wed, 22 Apr 2020 10:52:50: 36000000 INFO @ Wed, 22 Apr 2020 10:52:51: 42000000 INFO @ Wed, 22 Apr 2020 10:52:52: 31000000 INFO @ Wed, 22 Apr 2020 10:52:56: 37000000 INFO @ Wed, 22 Apr 2020 10:52:56: 43000000 INFO @ Wed, 22 Apr 2020 10:52:58: 32000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:53:01: 38000000 INFO @ Wed, 22 Apr 2020 10:53:02: 44000000 INFO @ Wed, 22 Apr 2020 10:53:03: 33000000 INFO @ Wed, 22 Apr 2020 10:53:07: 39000000 INFO @ Wed, 22 Apr 2020 10:53:08: 45000000 INFO @ Wed, 22 Apr 2020 10:53:09: 34000000 INFO @ Wed, 22 Apr 2020 10:53:13: 40000000 INFO @ Wed, 22 Apr 2020 10:53:13: 46000000 INFO @ Wed, 22 Apr 2020 10:53:14: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:53:14: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:53:14: #1 total tags in treatment: 22847950 INFO @ Wed, 22 Apr 2020 10:53:14: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:53:14: #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 10:53:14: #1 tags after filtering in treatment: 13735096 INFO @ Wed, 22 Apr 2020 10:53:14: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 10:53:14: #1 finished! INFO @ Wed, 22 Apr 2020 10:53:14: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:53:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:53:15: 35000000 INFO @ Wed, 22 Apr 2020 10:53:15: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:53:15: 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 10:53:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.05_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/SRX7409580/SRX7409580.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:53:18: 41000000 INFO @ Wed, 22 Apr 2020 10:53:20: 36000000 INFO @ Wed, 22 Apr 2020 10:53:24: 42000000 INFO @ Wed, 22 Apr 2020 10:53:26: 37000000 INFO @ Wed, 22 Apr 2020 10:53:29: 43000000 INFO @ Wed, 22 Apr 2020 10:53:31: 38000000 INFO @ Wed, 22 Apr 2020 10:53:34: 44000000 INFO @ Wed, 22 Apr 2020 10:53:36: 39000000 INFO @ Wed, 22 Apr 2020 10:53:40: 45000000 INFO @ Wed, 22 Apr 2020 10:53:42: 40000000 INFO @ Wed, 22 Apr 2020 10:53:45: 46000000 INFO @ Wed, 22 Apr 2020 10:53:46: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:53:46: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:53:46: #1 total tags in treatment: 22847950 INFO @ Wed, 22 Apr 2020 10:53:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:53:46: #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 10:53:46: #1 tags after filtering in treatment: 13735096 INFO @ Wed, 22 Apr 2020 10:53:46: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 10:53:46: #1 finished! INFO @ Wed, 22 Apr 2020 10:53:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:53:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:53:47: 41000000 INFO @ Wed, 22 Apr 2020 10:53:47: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:53:47: 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 10:53:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.10_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/SRX7409580/SRX7409580.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:53:52: 42000000 INFO @ Wed, 22 Apr 2020 10:53:57: 43000000 INFO @ Wed, 22 Apr 2020 10:54:02: 44000000 INFO @ Wed, 22 Apr 2020 10:54:07: 45000000 INFO @ Wed, 22 Apr 2020 10:54:12: 46000000 INFO @ Wed, 22 Apr 2020 10:54:13: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:54:13: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:54:13: #1 total tags in treatment: 22847950 INFO @ Wed, 22 Apr 2020 10:54:13: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:54:13: #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 10:54:13: #1 tags after filtering in treatment: 13735096 INFO @ Wed, 22 Apr 2020 10:54:13: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 10:54:13: #1 finished! INFO @ Wed, 22 Apr 2020 10:54:13: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:54:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:54:14: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:54:14: 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 10:54:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.20_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/SRX7409580/SRX7409580.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409580/SRX7409580.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling