Job ID = 6497571 SRX = SRX747297 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:08:48 prefetch.2.10.7: 1) Downloading 'SRR1634995'... 2020-06-25T23:08:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:10:29 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:10:29 prefetch.2.10.7: 'SRR1634995' is valid 2020-06-25T23:10:29 prefetch.2.10.7: 1) 'SRR1634995' was downloaded successfully 2020-06-25T23:11:02 prefetch.2.10.7: 'SRR1634995' has 6 unresolved dependencies 2020-06-25T23:11:02 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-25T23:11:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:11:17 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:11:17 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T23:11:17 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-25T23:11:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:11:33 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:11:33 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T23:11:33 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-25T23:11:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:16:44 prefetch.2.10.7 int: connection failed while opening file within cryptographic module - Cannot KNSManagerMakeClientRequest: https://sra-download.ncbi.nlm.nih.gov/traces/refseq/BX284603.3 2020-06-25T23:16:44 prefetch.2.10.7: HTTPS download failed 2020-06-25T23:16:44 prefetch.2.10.7: 4) failed to download ncbi-acc:BX284603.3?vdb-ctx=refseq 2020-06-25T23:22:01 fastq-dump.2.10.7 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/refseq/BX284604.3' 2020-06-25T23:22:15 fastq-dump.2.10.7 err: data corrupt while selecting function within transform module - failed SRR1634995/SRR1634995.sra ============================================================= An error occurred during processing. A report was generated into the file '/home/okishinya/ncbi_error_report.txt'. If the problem persists, you may consider sending the file to 'sra-tools@ncbi.nlm.nih.gov' for assistance. ============================================================= fastq-dump quit with error code 3 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:42 4421632 reads; of these: 4421632 (100.00%) were unpaired; of these: 74751 (1.69%) aligned 0 times 3615852 (81.78%) aligned exactly 1 time 731029 (16.53%) aligned >1 times 98.31% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 551968 / 4346881 = 0.1270 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 @ Fri, 26 Jun 2020 08:24:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.bam'] # control file = None # effective genome size = 9.00e+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 @ Fri, 26 Jun 2020 08:24:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:24:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:24:59: 1000000 INFO @ Fri, 26 Jun 2020 08:25:04: 2000000 INFO @ Fri, 26 Jun 2020 08:25:08: 3000000 INFO @ Fri, 26 Jun 2020 08:25:12: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 08:25:12: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 08:25:12: #1 total tags in treatment: 3794913 INFO @ Fri, 26 Jun 2020 08:25:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:25:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:25:12: #1 tags after filtering in treatment: 3794913 INFO @ Fri, 26 Jun 2020 08:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:25:12: #1 finished! INFO @ Fri, 26 Jun 2020 08:25:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:25:12: #2 number of paired peaks: 306 WARNING @ Fri, 26 Jun 2020 08:25:12: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Fri, 26 Jun 2020 08:25:12: start model_add_line... INFO @ Fri, 26 Jun 2020 08:25:12: start X-correlation... INFO @ Fri, 26 Jun 2020 08:25:13: end of X-cor INFO @ Fri, 26 Jun 2020 08:25:13: #2 finished! INFO @ Fri, 26 Jun 2020 08:25:13: #2 predicted fragment length is 36 bps INFO @ Fri, 26 Jun 2020 08:25:13: #2 alternative fragment length(s) may be 4,36,510,557,598 bps INFO @ Fri, 26 Jun 2020 08:25:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.05_model.r WARNING @ Fri, 26 Jun 2020 08:25:13: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:25:13: #2 You may need to consider one of the other alternative d(s): 4,36,510,557,598 WARNING @ Fri, 26 Jun 2020 08:25:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:25:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:25:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:25:19: #3 Call peaks for each chromosome... 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 @ Fri, 26 Jun 2020 08:25:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.05_summits.bed INFO @ Fri, 26 Jun 2020 08:25:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (343 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.bam'] # control file = None # effective genome size = 9.00e+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 @ Fri, 26 Jun 2020 08:25:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:25:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:25:29: 1000000 INFO @ Fri, 26 Jun 2020 08:25:34: 2000000 INFO @ Fri, 26 Jun 2020 08:25:39: 3000000 INFO @ Fri, 26 Jun 2020 08:25:42: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 08:25:42: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 08:25:42: #1 total tags in treatment: 3794913 INFO @ Fri, 26 Jun 2020 08:25:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:25:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:25:42: #1 tags after filtering in treatment: 3794913 INFO @ Fri, 26 Jun 2020 08:25:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:25:42: #1 finished! INFO @ Fri, 26 Jun 2020 08:25:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:25:43: #2 number of paired peaks: 306 WARNING @ Fri, 26 Jun 2020 08:25:43: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Fri, 26 Jun 2020 08:25:43: start model_add_line... INFO @ Fri, 26 Jun 2020 08:25:43: start X-correlation... INFO @ Fri, 26 Jun 2020 08:25:43: end of X-cor INFO @ Fri, 26 Jun 2020 08:25:43: #2 finished! INFO @ Fri, 26 Jun 2020 08:25:43: #2 predicted fragment length is 36 bps INFO @ Fri, 26 Jun 2020 08:25:43: #2 alternative fragment length(s) may be 4,36,510,557,598 bps INFO @ Fri, 26 Jun 2020 08:25:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.10_model.r WARNING @ Fri, 26 Jun 2020 08:25:43: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:25:43: #2 You may need to consider one of the other alternative d(s): 4,36,510,557,598 WARNING @ Fri, 26 Jun 2020 08:25:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:25:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:25:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:25:50: #3 Call peaks for each chromosome... 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 @ Fri, 26 Jun 2020 08:25:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:25:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:25:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.10_summits.bed INFO @ Fri, 26 Jun 2020 08:25:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:25:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.bam'] # control file = None # effective genome size = 9.00e+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 @ Fri, 26 Jun 2020 08:25:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:25:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:25:59: 1000000 INFO @ Fri, 26 Jun 2020 08:26:04: 2000000 INFO @ Fri, 26 Jun 2020 08:26:09: 3000000 INFO @ Fri, 26 Jun 2020 08:26:13: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 08:26:13: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 08:26:13: #1 total tags in treatment: 3794913 INFO @ Fri, 26 Jun 2020 08:26:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:26:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:26:13: #1 tags after filtering in treatment: 3794913 INFO @ Fri, 26 Jun 2020 08:26:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:26:13: #1 finished! INFO @ Fri, 26 Jun 2020 08:26:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:26:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:26:13: #2 number of paired peaks: 306 WARNING @ Fri, 26 Jun 2020 08:26:13: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Fri, 26 Jun 2020 08:26:13: start model_add_line... INFO @ Fri, 26 Jun 2020 08:26:13: start X-correlation... INFO @ Fri, 26 Jun 2020 08:26:13: end of X-cor INFO @ Fri, 26 Jun 2020 08:26:13: #2 finished! INFO @ Fri, 26 Jun 2020 08:26:13: #2 predicted fragment length is 36 bps INFO @ Fri, 26 Jun 2020 08:26:13: #2 alternative fragment length(s) may be 4,36,510,557,598 bps INFO @ Fri, 26 Jun 2020 08:26:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.20_model.r WARNING @ Fri, 26 Jun 2020 08:26:13: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:26:13: #2 You may need to consider one of the other alternative d(s): 4,36,510,557,598 WARNING @ Fri, 26 Jun 2020 08:26:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:26:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:26:13: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:26:20: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747297/SRX747297.20_summits.bed INFO @ Fri, 26 Jun 2020 08:26:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (37 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。