Job ID = 5790816 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,387,201 reads read : 1,387,201 reads written : 1,387,201 spots read : 1,311,060 reads read : 1,311,060 reads written : 1,311,060 spots read : 1,303,037 reads read : 1,303,037 reads written : 1,303,037 2020-04-21T22:41:11 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 ) 2020-04-21T22:41:11 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.235' from '172.19.7.208' 2020-04-21T22:41:11 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 '172.19.7.208' 2020-04-21T22:41:11 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/era0/ERR/ERR2851/ERR2851685' 2020-04-21T22:41:24 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'ERR2851685' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 1,252,900 reads read : 1,252,900 reads written : 1,252,900 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: 00:00:47 5254198 reads; of these: 5254198 (100.00%) were unpaired; of these: 100492 (1.91%) aligned 0 times 4040813 (76.91%) aligned exactly 1 time 1112893 (21.18%) aligned >1 times 98.09% overall alignment rate Time searching: 00:00:47 Overall time: 00:00:47 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] 5011516 / 5153706 = 0.9724 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 07:45:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.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 07:45:09: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:45:09: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:45:10: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:45:10: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:45:10: #1 total tags in treatment: 142190 INFO @ Wed, 22 Apr 2020 07:45:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:45:10: #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 07:45:10: #1 tags after filtering in treatment: 142190 INFO @ Wed, 22 Apr 2020 07:45:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:45:10: #1 finished! INFO @ Wed, 22 Apr 2020 07:45:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:45:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:45:10: #2 number of paired peaks: 399 WARNING @ Wed, 22 Apr 2020 07:45:10: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Wed, 22 Apr 2020 07:45:10: start model_add_line... INFO @ Wed, 22 Apr 2020 07:45:10: start X-correlation... INFO @ Wed, 22 Apr 2020 07:45:10: end of X-cor INFO @ Wed, 22 Apr 2020 07:45:10: #2 finished! INFO @ Wed, 22 Apr 2020 07:45:10: #2 predicted fragment length is 133 bps INFO @ Wed, 22 Apr 2020 07:45:10: #2 alternative fragment length(s) may be 13,72,87,133,192,215,251,273,287,313,455,483,506,560,584 bps INFO @ Wed, 22 Apr 2020 07:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.05_model.r WARNING @ Wed, 22 Apr 2020 07:45:10: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:45:10: #2 You may need to consider one of the other alternative d(s): 13,72,87,133,192,215,251,273,287,313,455,483,506,560,584 WARNING @ Wed, 22 Apr 2020 07:45:10: #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 07:45:10: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:45:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:45:10: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:45:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.05_summits.bed INFO @ Wed, 22 Apr 2020 07:45:10: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 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 07:45:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.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 07:45:39: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:45:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:45:40: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:45:40: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:45:40: #1 total tags in treatment: 142190 INFO @ Wed, 22 Apr 2020 07:45:40: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:45:40: #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 07:45:40: #1 tags after filtering in treatment: 142190 INFO @ Wed, 22 Apr 2020 07:45:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:45:40: #1 finished! INFO @ Wed, 22 Apr 2020 07:45:40: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:45:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:45:40: #2 number of paired peaks: 399 WARNING @ Wed, 22 Apr 2020 07:45:40: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Wed, 22 Apr 2020 07:45:40: start model_add_line... INFO @ Wed, 22 Apr 2020 07:45:40: start X-correlation... INFO @ Wed, 22 Apr 2020 07:45:40: end of X-cor INFO @ Wed, 22 Apr 2020 07:45:40: #2 finished! INFO @ Wed, 22 Apr 2020 07:45:40: #2 predicted fragment length is 133 bps INFO @ Wed, 22 Apr 2020 07:45:40: #2 alternative fragment length(s) may be 13,72,87,133,192,215,251,273,287,313,455,483,506,560,584 bps INFO @ Wed, 22 Apr 2020 07:45:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.10_model.r WARNING @ Wed, 22 Apr 2020 07:45:40: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:45:40: #2 You may need to consider one of the other alternative d(s): 13,72,87,133,192,215,251,273,287,313,455,483,506,560,584 WARNING @ Wed, 22 Apr 2020 07:45:40: #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 07:45:40: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:45:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:45:40: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:45:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:45:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:45:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.10_summits.bed INFO @ Wed, 22 Apr 2020 07:45:40: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (24 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 07:46:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.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 07:46:09: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:46:09: #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 07:46:10: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:46:10: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:46:10: #1 total tags in treatment: 142190 INFO @ Wed, 22 Apr 2020 07:46:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:46:10: #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 07:46:10: #1 tags after filtering in treatment: 142190 INFO @ Wed, 22 Apr 2020 07:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:46:10: #1 finished! INFO @ Wed, 22 Apr 2020 07:46:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:46:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:46:10: #2 number of paired peaks: 399 WARNING @ Wed, 22 Apr 2020 07:46:10: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Wed, 22 Apr 2020 07:46:10: start model_add_line... INFO @ Wed, 22 Apr 2020 07:46:10: start X-correlation... INFO @ Wed, 22 Apr 2020 07:46:10: end of X-cor INFO @ Wed, 22 Apr 2020 07:46:10: #2 finished! INFO @ Wed, 22 Apr 2020 07:46:10: #2 predicted fragment length is 133 bps INFO @ Wed, 22 Apr 2020 07:46:10: #2 alternative fragment length(s) may be 13,72,87,133,192,215,251,273,287,313,455,483,506,560,584 bps INFO @ Wed, 22 Apr 2020 07:46:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.20_model.r WARNING @ Wed, 22 Apr 2020 07:46:10: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:46:10: #2 You may need to consider one of the other alternative d(s): 13,72,87,133,192,215,251,273,287,313,455,483,506,560,584 WARNING @ Wed, 22 Apr 2020 07:46:10: #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 07:46:10: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:46:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:46:10: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:46:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:46:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:46:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858295/ERX2858295.20_summits.bed INFO @ Wed, 22 Apr 2020 07:46:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling