Job ID = 5791315 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:28:08 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 ) 2020-04-22T00:32:37 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 ) 2020-04-22T00:32:37 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 ) 2020-04-22T00:32:37 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 ) 2020-04-22T00:39:38 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 ) spots read : 24,545,621 reads read : 49,091,242 reads written : 49,091,242 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: 00:12:57 24545621 reads; of these: 24545621 (100.00%) were paired; of these: 712857 (2.90%) aligned concordantly 0 times 20220976 (82.38%) aligned concordantly exactly 1 time 3611788 (14.71%) aligned concordantly >1 times ---- 712857 pairs aligned concordantly 0 times; of these: 70068 (9.83%) aligned discordantly 1 time ---- 642789 pairs aligned 0 times concordantly or discordantly; of these: 1285578 mates make up the pairs; of these: 948612 (73.79%) aligned 0 times 259862 (20.21%) aligned exactly 1 time 77104 (6.00%) aligned >1 times 98.07% overall alignment rate Time searching: 00:12:57 Overall time: 00:12:57 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 20 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] 5002763 / 23847793 = 0.2098 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 10:03:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.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 10:03:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:03:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:03:44: 1000000 INFO @ Wed, 22 Apr 2020 10:03:51: 2000000 INFO @ Wed, 22 Apr 2020 10:03:57: 3000000 INFO @ Wed, 22 Apr 2020 10:04:03: 4000000 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 10:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.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 10:04:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:04:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:04:10: 5000000 INFO @ Wed, 22 Apr 2020 10:04:15: 1000000 INFO @ Wed, 22 Apr 2020 10:04:17: 6000000 INFO @ Wed, 22 Apr 2020 10:04:22: 2000000 INFO @ Wed, 22 Apr 2020 10:04:24: 7000000 INFO @ Wed, 22 Apr 2020 10:04:28: 3000000 INFO @ Wed, 22 Apr 2020 10:04:31: 8000000 INFO @ Wed, 22 Apr 2020 10:04:36: 4000000 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 10:04:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.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 10:04:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:04:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:04:38: 9000000 INFO @ Wed, 22 Apr 2020 10:04:42: 5000000 INFO @ Wed, 22 Apr 2020 10:04:45: 1000000 INFO @ Wed, 22 Apr 2020 10:04:45: 10000000 INFO @ Wed, 22 Apr 2020 10:04:49: 6000000 INFO @ Wed, 22 Apr 2020 10:04:52: 2000000 INFO @ Wed, 22 Apr 2020 10:04:52: 11000000 INFO @ Wed, 22 Apr 2020 10:04:56: 7000000 INFO @ Wed, 22 Apr 2020 10:04:59: 3000000 INFO @ Wed, 22 Apr 2020 10:04:59: 12000000 INFO @ Wed, 22 Apr 2020 10:05:03: 8000000 INFO @ Wed, 22 Apr 2020 10:05:06: 4000000 INFO @ Wed, 22 Apr 2020 10:05:07: 13000000 INFO @ Wed, 22 Apr 2020 10:05:10: 9000000 INFO @ Wed, 22 Apr 2020 10:05:13: 5000000 INFO @ Wed, 22 Apr 2020 10:05:14: 14000000 INFO @ Wed, 22 Apr 2020 10:05:17: 10000000 INFO @ Wed, 22 Apr 2020 10:05:21: 15000000 INFO @ Wed, 22 Apr 2020 10:05:21: 6000000 INFO @ Wed, 22 Apr 2020 10:05:25: 11000000 INFO @ Wed, 22 Apr 2020 10:05:28: 16000000 INFO @ Wed, 22 Apr 2020 10:05:28: 7000000 INFO @ Wed, 22 Apr 2020 10:05:32: 12000000 INFO @ Wed, 22 Apr 2020 10:05:35: 17000000 INFO @ Wed, 22 Apr 2020 10:05:35: 8000000 INFO @ Wed, 22 Apr 2020 10:05:39: 13000000 INFO @ Wed, 22 Apr 2020 10:05:42: 18000000 INFO @ Wed, 22 Apr 2020 10:05:43: 9000000 INFO @ Wed, 22 Apr 2020 10:05:46: 14000000 INFO @ Wed, 22 Apr 2020 10:05:49: 19000000 INFO @ Wed, 22 Apr 2020 10:05:50: 10000000 INFO @ Wed, 22 Apr 2020 10:05:53: 15000000 INFO @ Wed, 22 Apr 2020 10:05:56: 20000000 INFO @ Wed, 22 Apr 2020 10:05:57: 11000000 INFO @ Wed, 22 Apr 2020 10:06:00: 16000000 INFO @ Wed, 22 Apr 2020 10:06:02: 21000000 INFO @ Wed, 22 Apr 2020 10:06:04: 12000000 INFO @ Wed, 22 Apr 2020 10:06:07: 17000000 INFO @ Wed, 22 Apr 2020 10:06:09: 22000000 INFO @ Wed, 22 Apr 2020 10:06:12: 13000000 INFO @ Wed, 22 Apr 2020 10:06:15: 18000000 INFO @ Wed, 22 Apr 2020 10:06:16: 23000000 INFO @ Wed, 22 Apr 2020 10:06:19: 14000000 INFO @ Wed, 22 Apr 2020 10:06:22: 19000000 INFO @ Wed, 22 Apr 2020 10:06:23: 24000000 INFO @ Wed, 22 Apr 2020 10:06:26: 15000000 INFO @ Wed, 22 Apr 2020 10:06:28: 20000000 INFO @ Wed, 22 Apr 2020 10:06:30: 25000000 INFO @ Wed, 22 Apr 2020 10:06:33: 16000000 INFO @ Wed, 22 Apr 2020 10:06:36: 21000000 INFO @ Wed, 22 Apr 2020 10:06:37: 26000000 INFO @ Wed, 22 Apr 2020 10:06:40: 17000000 INFO @ Wed, 22 Apr 2020 10:06:43: 22000000 INFO @ Wed, 22 Apr 2020 10:06:44: 27000000 INFO @ Wed, 22 Apr 2020 10:06:47: 18000000 INFO @ Wed, 22 Apr 2020 10:06:50: 23000000 INFO @ Wed, 22 Apr 2020 10:06:51: 28000000 INFO @ Wed, 22 Apr 2020 10:06:54: 19000000 INFO @ Wed, 22 Apr 2020 10:06:57: 24000000 INFO @ Wed, 22 Apr 2020 10:06:58: 29000000 INFO @ Wed, 22 Apr 2020 10:07:02: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:07:03: 25000000 INFO @ Wed, 22 Apr 2020 10:07:06: 30000000 INFO @ Wed, 22 Apr 2020 10:07:09: 21000000 INFO @ Wed, 22 Apr 2020 10:07:10: 26000000 INFO @ Wed, 22 Apr 2020 10:07:13: 31000000 INFO @ Wed, 22 Apr 2020 10:07:16: 22000000 INFO @ Wed, 22 Apr 2020 10:07:17: 27000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:07:20: 32000000 INFO @ Wed, 22 Apr 2020 10:07:23: 23000000 INFO @ Wed, 22 Apr 2020 10:07:24: 28000000 INFO @ Wed, 22 Apr 2020 10:07:27: 33000000 INFO @ Wed, 22 Apr 2020 10:07:30: 24000000 INFO @ Wed, 22 Apr 2020 10:07:31: 29000000 INFO @ Wed, 22 Apr 2020 10:07:34: 34000000 INFO @ Wed, 22 Apr 2020 10:07:36: 25000000 INFO @ Wed, 22 Apr 2020 10:07:38: 30000000 INFO @ Wed, 22 Apr 2020 10:07:41: 35000000 INFO @ Wed, 22 Apr 2020 10:07:43: 26000000 INFO @ Wed, 22 Apr 2020 10:07:45: 31000000 INFO @ Wed, 22 Apr 2020 10:07:48: 36000000 INFO @ Wed, 22 Apr 2020 10:07:50: 27000000 INFO @ Wed, 22 Apr 2020 10:07:52: 32000000 INFO @ Wed, 22 Apr 2020 10:07:55: 37000000 INFO @ Wed, 22 Apr 2020 10:07:57: 28000000 INFO @ Wed, 22 Apr 2020 10:07:59: 33000000 INFO @ Wed, 22 Apr 2020 10:08:02: 38000000 INFO @ Wed, 22 Apr 2020 10:08:03: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:08:03: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:08:03: #1 total tags in treatment: 18831792 INFO @ Wed, 22 Apr 2020 10:08:03: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:08:03: #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 10:08:03: #1 tags after filtering in treatment: 11743816 INFO @ Wed, 22 Apr 2020 10:08:03: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 10:08:03: #1 finished! INFO @ Wed, 22 Apr 2020 10:08:03: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:08:04: 29000000 INFO @ Wed, 22 Apr 2020 10:08:04: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:08:04: 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 10:08:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.05_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/SRX7409569/SRX7409569.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:08:06: 34000000 INFO @ Wed, 22 Apr 2020 10:08:11: 30000000 INFO @ Wed, 22 Apr 2020 10:08:13: 35000000 INFO @ Wed, 22 Apr 2020 10:08:18: 31000000 INFO @ Wed, 22 Apr 2020 10:08:19: 36000000 INFO @ Wed, 22 Apr 2020 10:08:25: 32000000 INFO @ Wed, 22 Apr 2020 10:08:26: 37000000 INFO @ Wed, 22 Apr 2020 10:08:32: 33000000 INFO @ Wed, 22 Apr 2020 10:08:32: 38000000 INFO @ Wed, 22 Apr 2020 10:08:33: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:08:33: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:08:33: #1 total tags in treatment: 18831792 INFO @ Wed, 22 Apr 2020 10:08:33: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:08:33: #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 10:08:34: #1 tags after filtering in treatment: 11743816 INFO @ Wed, 22 Apr 2020 10:08:34: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 10:08:34: #1 finished! INFO @ Wed, 22 Apr 2020 10:08:34: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:08:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:08:34: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:08:34: 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 10:08:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.10_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/SRX7409569/SRX7409569.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:08:38: 34000000 INFO @ Wed, 22 Apr 2020 10:08:45: 35000000 INFO @ Wed, 22 Apr 2020 10:08:51: 36000000 INFO @ Wed, 22 Apr 2020 10:08:57: 37000000 INFO @ Wed, 22 Apr 2020 10:09:03: 38000000 INFO @ Wed, 22 Apr 2020 10:09:04: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:09:04: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:09:04: #1 total tags in treatment: 18831792 INFO @ Wed, 22 Apr 2020 10:09:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:09:04: #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 10:09:04: #1 tags after filtering in treatment: 11743816 INFO @ Wed, 22 Apr 2020 10:09:04: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 10:09:04: #1 finished! INFO @ Wed, 22 Apr 2020 10:09:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:09:05: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:09:05: 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 10:09:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.20_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/SRX7409569/SRX7409569.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409569/SRX7409569.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling