Job ID = 5791290 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:21:45 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 ) 2020-04-22T00:21:45 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 ) 2020-04-22T00:22:34 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 ) 2020-04-22T00:22:34 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 ) 2020-04-22T00:32:29 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 ) 2020-04-22T00:32:29 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 : 34,772,092 reads read : 69,544,184 reads written : 69,544,184 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: 00:17:49 34772092 reads; of these: 34772092 (100.00%) were paired; of these: 956243 (2.75%) aligned concordantly 0 times 29878678 (85.93%) aligned concordantly exactly 1 time 3937171 (11.32%) aligned concordantly >1 times ---- 956243 pairs aligned concordantly 0 times; of these: 75342 (7.88%) aligned discordantly 1 time ---- 880901 pairs aligned 0 times concordantly or discordantly; of these: 1761802 mates make up the pairs; of these: 1449983 (82.30%) aligned 0 times 250711 (14.23%) aligned exactly 1 time 61108 (3.47%) aligned >1 times 97.92% overall alignment rate Time searching: 00:17:49 Overall time: 00:17:49 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] 10868787 / 33826472 = 0.3213 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 10:12:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.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 10:12:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:12:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:12:48: 1000000 INFO @ Wed, 22 Apr 2020 10:12:54: 2000000 INFO @ Wed, 22 Apr 2020 10:12:59: 3000000 INFO @ Wed, 22 Apr 2020 10:13:04: 4000000 INFO @ Wed, 22 Apr 2020 10:13:09: 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 10:13:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.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 10:13:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:13:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:13:15: 6000000 INFO @ Wed, 22 Apr 2020 10:13:20: 1000000 INFO @ Wed, 22 Apr 2020 10:13:22: 7000000 INFO @ Wed, 22 Apr 2020 10:13:28: 2000000 INFO @ Wed, 22 Apr 2020 10:13:28: 8000000 INFO @ Wed, 22 Apr 2020 10:13:35: 3000000 INFO @ Wed, 22 Apr 2020 10:13:35: 9000000 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 10:13:41: 10000000 INFO @ Wed, 22 Apr 2020 10:13:42: 4000000 INFO @ Wed, 22 Apr 2020 10:13:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.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 10:13:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:13:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:13:48: 11000000 INFO @ Wed, 22 Apr 2020 10:13:49: 5000000 INFO @ Wed, 22 Apr 2020 10:13:50: 1000000 INFO @ Wed, 22 Apr 2020 10:13:55: 12000000 INFO @ Wed, 22 Apr 2020 10:13:56: 6000000 INFO @ Wed, 22 Apr 2020 10:13:57: 2000000 INFO @ Wed, 22 Apr 2020 10:14:02: 13000000 INFO @ Wed, 22 Apr 2020 10:14:03: 7000000 INFO @ Wed, 22 Apr 2020 10:14:04: 3000000 INFO @ Wed, 22 Apr 2020 10:14:10: 14000000 INFO @ Wed, 22 Apr 2020 10:14:10: 8000000 INFO @ Wed, 22 Apr 2020 10:14:11: 4000000 INFO @ Wed, 22 Apr 2020 10:14:17: 15000000 INFO @ Wed, 22 Apr 2020 10:14:17: 9000000 INFO @ Wed, 22 Apr 2020 10:14:18: 5000000 INFO @ Wed, 22 Apr 2020 10:14:24: 16000000 INFO @ Wed, 22 Apr 2020 10:14:24: 10000000 INFO @ Wed, 22 Apr 2020 10:14:25: 6000000 INFO @ Wed, 22 Apr 2020 10:14:31: 17000000 INFO @ Wed, 22 Apr 2020 10:14:32: 11000000 INFO @ Wed, 22 Apr 2020 10:14:33: 7000000 INFO @ Wed, 22 Apr 2020 10:14:38: 18000000 INFO @ Wed, 22 Apr 2020 10:14:39: 12000000 INFO @ Wed, 22 Apr 2020 10:14:39: 8000000 INFO @ Wed, 22 Apr 2020 10:14:45: 19000000 INFO @ Wed, 22 Apr 2020 10:14:46: 13000000 INFO @ Wed, 22 Apr 2020 10:14:46: 9000000 INFO @ Wed, 22 Apr 2020 10:14:51: 20000000 INFO @ Wed, 22 Apr 2020 10:14:53: 10000000 INFO @ Wed, 22 Apr 2020 10:14:54: 14000000 INFO @ Wed, 22 Apr 2020 10:14:58: 21000000 INFO @ Wed, 22 Apr 2020 10:15:00: 11000000 INFO @ Wed, 22 Apr 2020 10:15:01: 15000000 INFO @ Wed, 22 Apr 2020 10:15:05: 22000000 INFO @ Wed, 22 Apr 2020 10:15:07: 12000000 INFO @ Wed, 22 Apr 2020 10:15:08: 16000000 INFO @ Wed, 22 Apr 2020 10:15:12: 23000000 INFO @ Wed, 22 Apr 2020 10:15:13: 13000000 INFO @ Wed, 22 Apr 2020 10:15:15: 17000000 INFO @ Wed, 22 Apr 2020 10:15:19: 24000000 INFO @ Wed, 22 Apr 2020 10:15:20: 14000000 INFO @ Wed, 22 Apr 2020 10:15:22: 18000000 INFO @ Wed, 22 Apr 2020 10:15:25: 25000000 INFO @ Wed, 22 Apr 2020 10:15:27: 15000000 INFO @ Wed, 22 Apr 2020 10:15:29: 19000000 INFO @ Wed, 22 Apr 2020 10:15:32: 26000000 INFO @ Wed, 22 Apr 2020 10:15:34: 16000000 INFO @ Wed, 22 Apr 2020 10:15:36: 20000000 INFO @ Wed, 22 Apr 2020 10:15:39: 27000000 INFO @ Wed, 22 Apr 2020 10:15:41: 17000000 INFO @ Wed, 22 Apr 2020 10:15:44: 21000000 INFO @ Wed, 22 Apr 2020 10:15:46: 28000000 INFO @ Wed, 22 Apr 2020 10:15:48: 18000000 INFO @ Wed, 22 Apr 2020 10:15:51: 22000000 INFO @ Wed, 22 Apr 2020 10:15:53: 29000000 INFO @ Wed, 22 Apr 2020 10:15:54: 19000000 INFO @ Wed, 22 Apr 2020 10:15:58: 23000000 INFO @ Wed, 22 Apr 2020 10:15:59: 30000000 INFO @ Wed, 22 Apr 2020 10:16:01: 20000000 INFO @ Wed, 22 Apr 2020 10:16:05: 24000000 INFO @ Wed, 22 Apr 2020 10:16:06: 31000000 INFO @ Wed, 22 Apr 2020 10:16:08: 21000000 INFO @ Wed, 22 Apr 2020 10:16:12: 25000000 INFO @ Wed, 22 Apr 2020 10:16:13: 32000000 INFO @ Wed, 22 Apr 2020 10:16:15: 22000000 INFO @ Wed, 22 Apr 2020 10:16:19: 26000000 INFO @ Wed, 22 Apr 2020 10:16:20: 33000000 INFO @ Wed, 22 Apr 2020 10:16:22: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:16:26: 27000000 INFO @ Wed, 22 Apr 2020 10:16:27: 34000000 INFO @ Wed, 22 Apr 2020 10:16:28: 24000000 INFO @ Wed, 22 Apr 2020 10:16:33: 28000000 INFO @ Wed, 22 Apr 2020 10:16:34: 35000000 INFO @ Wed, 22 Apr 2020 10:16:35: 25000000 INFO @ Wed, 22 Apr 2020 10:16:40: 29000000 INFO @ Wed, 22 Apr 2020 10:16:41: 36000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:16:42: 26000000 INFO @ Wed, 22 Apr 2020 10:16:47: 30000000 INFO @ Wed, 22 Apr 2020 10:16:47: 37000000 INFO @ Wed, 22 Apr 2020 10:16:49: 27000000 INFO @ Wed, 22 Apr 2020 10:16:54: 31000000 INFO @ Wed, 22 Apr 2020 10:16:54: 38000000 INFO @ Wed, 22 Apr 2020 10:16:56: 28000000 INFO @ Wed, 22 Apr 2020 10:17:01: 32000000 INFO @ Wed, 22 Apr 2020 10:17:01: 39000000 INFO @ Wed, 22 Apr 2020 10:17:03: 29000000 INFO @ Wed, 22 Apr 2020 10:17:08: 40000000 INFO @ Wed, 22 Apr 2020 10:17:08: 33000000 INFO @ Wed, 22 Apr 2020 10:17:09: 30000000 INFO @ Wed, 22 Apr 2020 10:17:14: 41000000 INFO @ Wed, 22 Apr 2020 10:17:15: 34000000 INFO @ Wed, 22 Apr 2020 10:17:16: 31000000 INFO @ Wed, 22 Apr 2020 10:17:21: 42000000 INFO @ Wed, 22 Apr 2020 10:17:22: 35000000 INFO @ Wed, 22 Apr 2020 10:17:23: 32000000 INFO @ Wed, 22 Apr 2020 10:17:28: 43000000 INFO @ Wed, 22 Apr 2020 10:17:29: 36000000 INFO @ Wed, 22 Apr 2020 10:17:30: 33000000 INFO @ Wed, 22 Apr 2020 10:17:35: 44000000 INFO @ Wed, 22 Apr 2020 10:17:36: 37000000 INFO @ Wed, 22 Apr 2020 10:17:37: 34000000 INFO @ Wed, 22 Apr 2020 10:17:42: 45000000 INFO @ Wed, 22 Apr 2020 10:17:43: 38000000 INFO @ Wed, 22 Apr 2020 10:17:44: 35000000 INFO @ Wed, 22 Apr 2020 10:17:49: 46000000 INFO @ Wed, 22 Apr 2020 10:17:50: 36000000 INFO @ Wed, 22 Apr 2020 10:17:51: 39000000 INFO @ Wed, 22 Apr 2020 10:17:51: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:17:51: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:17:51: #1 total tags in treatment: 22950781 INFO @ Wed, 22 Apr 2020 10:17:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:17:51: #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 10:17:52: #1 tags after filtering in treatment: 13464113 INFO @ Wed, 22 Apr 2020 10:17:52: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 10:17:52: #1 finished! INFO @ Wed, 22 Apr 2020 10:17:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:17:52: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:17:52: 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 10:17:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.05_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/SRX7409549/SRX7409549.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:17:57: 37000000 INFO @ Wed, 22 Apr 2020 10:17:58: 40000000 INFO @ Wed, 22 Apr 2020 10:18:03: 38000000 INFO @ Wed, 22 Apr 2020 10:18:05: 41000000 INFO @ Wed, 22 Apr 2020 10:18:09: 39000000 INFO @ Wed, 22 Apr 2020 10:18:12: 42000000 INFO @ Wed, 22 Apr 2020 10:18:16: 40000000 INFO @ Wed, 22 Apr 2020 10:18:19: 43000000 INFO @ Wed, 22 Apr 2020 10:18:22: 41000000 INFO @ Wed, 22 Apr 2020 10:18:26: 44000000 INFO @ Wed, 22 Apr 2020 10:18:28: 42000000 INFO @ Wed, 22 Apr 2020 10:18:33: 45000000 INFO @ Wed, 22 Apr 2020 10:18:35: 43000000 INFO @ Wed, 22 Apr 2020 10:18:40: 46000000 INFO @ Wed, 22 Apr 2020 10:18:41: 44000000 INFO @ Wed, 22 Apr 2020 10:18:42: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:18:42: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:18:42: #1 total tags in treatment: 22950781 INFO @ Wed, 22 Apr 2020 10:18:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:18:42: #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 10:18:43: #1 tags after filtering in treatment: 13464113 INFO @ Wed, 22 Apr 2020 10:18:43: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 10:18:43: #1 finished! INFO @ Wed, 22 Apr 2020 10:18:43: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:18:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:18:43: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:18:43: 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 10:18:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.10_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/SRX7409549/SRX7409549.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:18:47: 45000000 INFO @ Wed, 22 Apr 2020 10:18:53: 46000000 INFO @ Wed, 22 Apr 2020 10:18:55: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:18:55: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:18:55: #1 total tags in treatment: 22950781 INFO @ Wed, 22 Apr 2020 10:18:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:18:55: #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 10:18:55: #1 tags after filtering in treatment: 13464113 INFO @ Wed, 22 Apr 2020 10:18:55: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 10:18:55: #1 finished! INFO @ Wed, 22 Apr 2020 10:18:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:18:56: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:18:56: 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 10:18:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.20_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/SRX7409549/SRX7409549.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409549/SRX7409549.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling