Job ID = 5790823 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,191,966 reads read : 2,191,966 reads written : 2,191,966 spots read : 2,080,585 reads read : 2,080,585 reads written : 2,080,585 2020-04-21T22:43:12 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-21T22:43:12 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-21T22:43:50 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2020-04-21T22:43:50 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.235' from '172.19.7.197' 2020-04-21T22:43:50 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (165.112.9.235) from '172.19.7.197' spots read : 2,068,150 reads read : 2,068,150 reads written : 2,068,150 spots read : 1,989,198 reads read : 1,989,198 reads written : 1,989,198 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: 00:01:14 8329899 reads; of these: 8329899 (100.00%) were unpaired; of these: 177104 (2.13%) aligned 0 times 6698158 (80.41%) aligned exactly 1 time 1454637 (17.46%) aligned >1 times 97.87% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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_rmdupse_core] 7929586 / 8152795 = 0.9726 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 07:49:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.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 07:49:47: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:49:47: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:49:48: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:49:48: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:49:48: #1 total tags in treatment: 223209 INFO @ Wed, 22 Apr 2020 07:49:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:49:48: #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 07:49:48: #1 tags after filtering in treatment: 223209 INFO @ Wed, 22 Apr 2020 07:49:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:49:48: #1 finished! INFO @ Wed, 22 Apr 2020 07:49:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:49:48: #2 number of paired peaks: 458 WARNING @ Wed, 22 Apr 2020 07:49:48: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Wed, 22 Apr 2020 07:49:48: start model_add_line... INFO @ Wed, 22 Apr 2020 07:49:48: start X-correlation... INFO @ Wed, 22 Apr 2020 07:49:48: end of X-cor INFO @ Wed, 22 Apr 2020 07:49:48: #2 finished! INFO @ Wed, 22 Apr 2020 07:49:48: #2 predicted fragment length is 87 bps INFO @ Wed, 22 Apr 2020 07:49:48: #2 alternative fragment length(s) may be 38,87,127,220,245,263,443,459,493,507,552 bps INFO @ Wed, 22 Apr 2020 07:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.05_model.r WARNING @ Wed, 22 Apr 2020 07:49:48: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:49:48: #2 You may need to consider one of the other alternative d(s): 38,87,127,220,245,263,443,459,493,507,552 WARNING @ Wed, 22 Apr 2020 07:49:48: #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 07:49:48: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:49:49: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:49:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:49:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:49:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.05_summits.bed INFO @ Wed, 22 Apr 2020 07:49:49: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (85 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.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 07:50:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:50:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:50:18: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:50:18: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:50:18: #1 total tags in treatment: 223209 INFO @ Wed, 22 Apr 2020 07:50:18: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:50:18: #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 07:50:18: #1 tags after filtering in treatment: 223209 INFO @ Wed, 22 Apr 2020 07:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:50:18: #1 finished! INFO @ Wed, 22 Apr 2020 07:50:18: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:50:18: #2 number of paired peaks: 458 WARNING @ Wed, 22 Apr 2020 07:50:18: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Wed, 22 Apr 2020 07:50:18: start model_add_line... INFO @ Wed, 22 Apr 2020 07:50:18: start X-correlation... INFO @ Wed, 22 Apr 2020 07:50:18: end of X-cor INFO @ Wed, 22 Apr 2020 07:50:18: #2 finished! INFO @ Wed, 22 Apr 2020 07:50:18: #2 predicted fragment length is 87 bps INFO @ Wed, 22 Apr 2020 07:50:18: #2 alternative fragment length(s) may be 38,87,127,220,245,263,443,459,493,507,552 bps INFO @ Wed, 22 Apr 2020 07:50:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.10_model.r WARNING @ Wed, 22 Apr 2020 07:50:18: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:50:18: #2 You may need to consider one of the other alternative d(s): 38,87,127,220,245,263,443,459,493,507,552 WARNING @ Wed, 22 Apr 2020 07:50:18: #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 07:50:18: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:50:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:50:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:50:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:50:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:50:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.10_summits.bed INFO @ Wed, 22 Apr 2020 07:50:19: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (34 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.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 07:50:45: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:50:45: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 07:50:46: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:50:46: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:50:46: #1 total tags in treatment: 223209 INFO @ Wed, 22 Apr 2020 07:50:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:50:46: #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 07:50:46: #1 tags after filtering in treatment: 223209 INFO @ Wed, 22 Apr 2020 07:50:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:50:46: #1 finished! INFO @ Wed, 22 Apr 2020 07:50:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:50:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:50:46: #2 number of paired peaks: 458 WARNING @ Wed, 22 Apr 2020 07:50:46: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Wed, 22 Apr 2020 07:50:46: start model_add_line... INFO @ Wed, 22 Apr 2020 07:50:46: start X-correlation... INFO @ Wed, 22 Apr 2020 07:50:46: end of X-cor INFO @ Wed, 22 Apr 2020 07:50:46: #2 finished! INFO @ Wed, 22 Apr 2020 07:50:46: #2 predicted fragment length is 87 bps INFO @ Wed, 22 Apr 2020 07:50:46: #2 alternative fragment length(s) may be 38,87,127,220,245,263,443,459,493,507,552 bps INFO @ Wed, 22 Apr 2020 07:50:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.20_model.r WARNING @ Wed, 22 Apr 2020 07:50:47: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:50:47: #2 You may need to consider one of the other alternative d(s): 38,87,127,220,245,263,443,459,493,507,552 WARNING @ Wed, 22 Apr 2020 07:50:47: #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 07:50:47: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:50:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:50:47: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:50:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:50:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:50:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858300/ERX2858300.20_summits.bed INFO @ Wed, 22 Apr 2020 07:50:47: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling