Job ID = 5791739 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:41:35 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 ) 1900-01-00T00:00:00 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 ) 2020-04-22T01:42:52 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 ) 2020-04-22T01:42:52 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 ) spots read : 4,003,648 reads read : 8,007,296 reads written : 8,007,296 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: 00:02:49 4003648 reads; of these: 4003648 (100.00%) were paired; of these: 264089 (6.60%) aligned concordantly 0 times 3252492 (81.24%) aligned concordantly exactly 1 time 487067 (12.17%) aligned concordantly >1 times ---- 264089 pairs aligned concordantly 0 times; of these: 106717 (40.41%) aligned discordantly 1 time ---- 157372 pairs aligned 0 times concordantly or discordantly; of these: 314744 mates make up the pairs; of these: 245458 (77.99%) aligned 0 times 30672 (9.75%) aligned exactly 1 time 38614 (12.27%) aligned >1 times 96.93% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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_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] 103241 / 3835995 = 0.0269 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 10:50:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.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 10:50:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:50:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:50:27: 1000000 INFO @ Wed, 22 Apr 2020 10:50:34: 2000000 INFO @ Wed, 22 Apr 2020 10:50:40: 3000000 INFO @ Wed, 22 Apr 2020 10:50:46: 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 10:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.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 10:50:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:50:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:50:52: 5000000 INFO @ Wed, 22 Apr 2020 10:50:56: 1000000 INFO @ Wed, 22 Apr 2020 10:50:59: 6000000 INFO @ Wed, 22 Apr 2020 10:51:02: 2000000 INFO @ Wed, 22 Apr 2020 10:51:05: 7000000 INFO @ Wed, 22 Apr 2020 10:51:09: 3000000 INFO @ Wed, 22 Apr 2020 10:51:09: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:51:09: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:51:09: #1 total tags in treatment: 3638273 INFO @ Wed, 22 Apr 2020 10:51:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:51:09: #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 10:51:09: #1 tags after filtering in treatment: 3042259 INFO @ Wed, 22 Apr 2020 10:51:09: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 22 Apr 2020 10:51:09: #1 finished! INFO @ Wed, 22 Apr 2020 10:51:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:51:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:51:09: #2 number of paired peaks: 122 WARNING @ Wed, 22 Apr 2020 10:51:09: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Wed, 22 Apr 2020 10:51:09: start model_add_line... INFO @ Wed, 22 Apr 2020 10:51:09: start X-correlation... INFO @ Wed, 22 Apr 2020 10:51:09: end of X-cor INFO @ Wed, 22 Apr 2020 10:51:09: #2 finished! INFO @ Wed, 22 Apr 2020 10:51:09: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Apr 2020 10:51:09: #2 alternative fragment length(s) may be 0,32,56,79,93,110,149,166,184,197,216,252,270,295,330,347,367,394,419,447,469,492,511,528,553,573,587 bps INFO @ Wed, 22 Apr 2020 10:51:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.05_model.r WARNING @ Wed, 22 Apr 2020 10:51:09: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 10:51:09: #2 You may need to consider one of the other alternative d(s): 0,32,56,79,93,110,149,166,184,197,216,252,270,295,330,347,367,394,419,447,469,492,511,528,553,573,587 WARNING @ Wed, 22 Apr 2020 10:51:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 10:51:09: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:51:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 10:51:15: 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 10:51:21: 5000000 INFO @ Wed, 22 Apr 2020 10:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.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 10:51:21: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:51:21: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:51:27: 1000000 INFO @ Wed, 22 Apr 2020 10:51:27: 6000000 INFO @ Wed, 22 Apr 2020 10:51:33: 7000000 INFO @ Wed, 22 Apr 2020 10:51:33: 2000000 INFO @ Wed, 22 Apr 2020 10:51:36: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:51:36: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:51:36: #1 total tags in treatment: 3638273 INFO @ Wed, 22 Apr 2020 10:51:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:51:36: #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 10:51:36: #1 tags after filtering in treatment: 3042259 INFO @ Wed, 22 Apr 2020 10:51:36: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 22 Apr 2020 10:51:36: #1 finished! INFO @ Wed, 22 Apr 2020 10:51:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:51:37: #2 number of paired peaks: 122 WARNING @ Wed, 22 Apr 2020 10:51:37: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Wed, 22 Apr 2020 10:51:37: start model_add_line... INFO @ Wed, 22 Apr 2020 10:51:37: start X-correlation... INFO @ Wed, 22 Apr 2020 10:51:37: end of X-cor INFO @ Wed, 22 Apr 2020 10:51:37: #2 finished! INFO @ Wed, 22 Apr 2020 10:51:37: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Apr 2020 10:51:37: #2 alternative fragment length(s) may be 0,32,56,79,93,110,149,166,184,197,216,252,270,295,330,347,367,394,419,447,469,492,511,528,553,573,587 bps INFO @ Wed, 22 Apr 2020 10:51:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.10_model.r WARNING @ Wed, 22 Apr 2020 10:51:37: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 10:51:37: #2 You may need to consider one of the other alternative d(s): 0,32,56,79,93,110,149,166,184,197,216,252,270,295,330,347,367,394,419,447,469,492,511,528,553,573,587 WARNING @ Wed, 22 Apr 2020 10:51:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 10:51:37: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:51:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 10:51:40: 3000000 INFO @ Wed, 22 Apr 2020 10:51:46: 4000000 INFO @ Wed, 22 Apr 2020 10:51:52: 5000000 INFO @ Wed, 22 Apr 2020 10:51:58: 6000000 INFO @ Wed, 22 Apr 2020 10:52:04: 7000000 INFO @ Wed, 22 Apr 2020 10:52:08: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:52:08: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:52:08: #1 total tags in treatment: 3638273 INFO @ Wed, 22 Apr 2020 10:52:08: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:52:08: #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 10:52:08: #1 tags after filtering in treatment: 3042259 INFO @ Wed, 22 Apr 2020 10:52:08: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 22 Apr 2020 10:52:08: #1 finished! INFO @ Wed, 22 Apr 2020 10:52:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:52:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:52:08: #2 number of paired peaks: 122 WARNING @ Wed, 22 Apr 2020 10:52:08: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Wed, 22 Apr 2020 10:52:08: start model_add_line... INFO @ Wed, 22 Apr 2020 10:52:08: start X-correlation... INFO @ Wed, 22 Apr 2020 10:52:08: end of X-cor INFO @ Wed, 22 Apr 2020 10:52:08: #2 finished! INFO @ Wed, 22 Apr 2020 10:52:08: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Apr 2020 10:52:08: #2 alternative fragment length(s) may be 0,32,56,79,93,110,149,166,184,197,216,252,270,295,330,347,367,394,419,447,469,492,511,528,553,573,587 bps INFO @ Wed, 22 Apr 2020 10:52:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741025/SRX7741025.20_model.r WARNING @ Wed, 22 Apr 2020 10:52:08: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 10:52:08: #2 You may need to consider one of the other alternative d(s): 0,32,56,79,93,110,149,166,184,197,216,252,270,295,330,347,367,394,419,447,469,492,511,528,553,573,587 WARNING @ Wed, 22 Apr 2020 10:52:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 10:52:08: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:52:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 /var/spool/uge/at154/job_scripts/5791739: line 336: 45003 Terminated MACS $i /var/spool/uge/at154/job_scripts/5791739: line 336: 46158 Terminated MACS $i /var/spool/uge/at154/job_scripts/5791739: line 336: 47351 Terminated MACS $i ls: cannot access SRX7741025.05.bed: No such file or directory mv: cannot stat ‘SRX7741025.05.bed’: No such file or directory mv: cannot stat ‘SRX7741025.05.bb’: No such file or directory ls: cannot access SRX7741025.10.bed: No such file or directory mv: cannot stat ‘SRX7741025.10.bed’: No such file or directory mv: cannot stat ‘SRX7741025.10.bb’: No such file or directory ls: cannot access SRX7741025.20.bed: No such file or directory mv: cannot stat ‘SRX7741025.20.bed’: No such file or directory mv: cannot stat ‘SRX7741025.20.bb’: No such file or directory