Job ID = 5790953 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:06:25 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 ) 2020-04-21T23:06:25 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 ) 2020-04-21T23:06:25 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 ) 2020-04-21T23:07:13 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 : 2,515,681 reads read : 5,031,362 reads written : 5,031,362 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: 00:00:01 Multiseed full-index search: 00:01:55 2515681 reads; of these: 2515681 (100.00%) were paired; of these: 139064 (5.53%) aligned concordantly 0 times 1723026 (68.49%) aligned concordantly exactly 1 time 653591 (25.98%) aligned concordantly >1 times ---- 139064 pairs aligned concordantly 0 times; of these: 5304 (3.81%) aligned discordantly 1 time ---- 133760 pairs aligned 0 times concordantly or discordantly; of these: 267520 mates make up the pairs; of these: 240989 (90.08%) aligned 0 times 14307 (5.35%) aligned exactly 1 time 12224 (4.57%) aligned >1 times 95.21% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 71280 / 2369280 = 0.0301 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 08:12:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.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 08:12:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:12:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:12:46: 1000000 INFO @ Wed, 22 Apr 2020 08:12:51: 2000000 INFO @ Wed, 22 Apr 2020 08:12:57: 3000000 INFO @ Wed, 22 Apr 2020 08:13:02: 4000000 INFO @ Wed, 22 Apr 2020 08:13:05: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:13:05: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:13:05: #1 total tags in treatment: 2305367 INFO @ Wed, 22 Apr 2020 08:13:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:05: #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 08:13:05: #1 tags after filtering in treatment: 1863154 INFO @ Wed, 22 Apr 2020 08:13:05: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 08:13:05: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:05: #2 number of paired peaks: 202 WARNING @ Wed, 22 Apr 2020 08:13:05: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Wed, 22 Apr 2020 08:13:05: start model_add_line... INFO @ Wed, 22 Apr 2020 08:13:05: start X-correlation... INFO @ Wed, 22 Apr 2020 08:13:05: end of X-cor INFO @ Wed, 22 Apr 2020 08:13:05: #2 finished! INFO @ Wed, 22 Apr 2020 08:13:05: #2 predicted fragment length is 141 bps INFO @ Wed, 22 Apr 2020 08:13:05: #2 alternative fragment length(s) may be 2,141,160,172 bps INFO @ Wed, 22 Apr 2020 08:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.05_model.r WARNING @ Wed, 22 Apr 2020 08:13:05: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:13:05: #2 You may need to consider one of the other alternative d(s): 2,141,160,172 WARNING @ Wed, 22 Apr 2020 08:13:05: #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 08:13:05: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:13:05: #3 Pre-compute pvalue-qvalue table... 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 08:13:10: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:13:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.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 08:13:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:13:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:13:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.05_summits.bed INFO @ Wed, 22 Apr 2020 08:13:12: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (424 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:13:16: 1000000 INFO @ Wed, 22 Apr 2020 08:13:21: 2000000 INFO @ Wed, 22 Apr 2020 08:13:27: 3000000 INFO @ Wed, 22 Apr 2020 08:13:32: 4000000 INFO @ Wed, 22 Apr 2020 08:13:35: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:13:35: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:13:35: #1 total tags in treatment: 2305367 INFO @ Wed, 22 Apr 2020 08:13:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:35: #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 08:13:35: #1 tags after filtering in treatment: 1863154 INFO @ Wed, 22 Apr 2020 08:13:35: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 08:13:35: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:35: #2 number of paired peaks: 202 WARNING @ Wed, 22 Apr 2020 08:13:35: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Wed, 22 Apr 2020 08:13:35: start model_add_line... INFO @ Wed, 22 Apr 2020 08:13:35: start X-correlation... INFO @ Wed, 22 Apr 2020 08:13:35: end of X-cor INFO @ Wed, 22 Apr 2020 08:13:35: #2 finished! INFO @ Wed, 22 Apr 2020 08:13:35: #2 predicted fragment length is 141 bps INFO @ Wed, 22 Apr 2020 08:13:35: #2 alternative fragment length(s) may be 2,141,160,172 bps INFO @ Wed, 22 Apr 2020 08:13:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.10_model.r WARNING @ Wed, 22 Apr 2020 08:13:35: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:13:35: #2 You may need to consider one of the other alternative d(s): 2,141,160,172 WARNING @ Wed, 22 Apr 2020 08:13:35: #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 08:13:35: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:13:35: #3 Pre-compute pvalue-qvalue table... 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 08:13:40: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:13:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.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 08:13:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:13:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:13:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.10_summits.bed INFO @ Wed, 22 Apr 2020 08:13:42: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:13:47: 1000000 INFO @ Wed, 22 Apr 2020 08:13:54: 2000000 INFO @ Wed, 22 Apr 2020 08:14:00: 3000000 INFO @ Wed, 22 Apr 2020 08:14:07: 4000000 INFO @ Wed, 22 Apr 2020 08:14:11: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:14:11: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:14:11: #1 total tags in treatment: 2305367 INFO @ Wed, 22 Apr 2020 08:14:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:14:11: #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 08:14:11: #1 tags after filtering in treatment: 1863154 INFO @ Wed, 22 Apr 2020 08:14:11: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 08:14:11: #1 finished! INFO @ Wed, 22 Apr 2020 08:14:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:14:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:14:11: #2 number of paired peaks: 202 WARNING @ Wed, 22 Apr 2020 08:14:11: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Wed, 22 Apr 2020 08:14:11: start model_add_line... INFO @ Wed, 22 Apr 2020 08:14:11: start X-correlation... INFO @ Wed, 22 Apr 2020 08:14:11: end of X-cor INFO @ Wed, 22 Apr 2020 08:14:11: #2 finished! INFO @ Wed, 22 Apr 2020 08:14:11: #2 predicted fragment length is 141 bps INFO @ Wed, 22 Apr 2020 08:14:11: #2 alternative fragment length(s) may be 2,141,160,172 bps INFO @ Wed, 22 Apr 2020 08:14:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.20_model.r WARNING @ Wed, 22 Apr 2020 08:14:11: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:14:11: #2 You may need to consider one of the other alternative d(s): 2,141,160,172 WARNING @ Wed, 22 Apr 2020 08:14:11: #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 08:14:11: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:14:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:14:16: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:14:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:14:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:14:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874468/SRX5874468.20_summits.bed INFO @ Wed, 22 Apr 2020 08:14:17: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (91 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。