Job ID = 6498241 SRX = SRX4315051 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:24:32 prefetch.2.10.7: 1) Downloading 'SRR7444512'... 2020-06-25T23:24:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:26:23 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:26:24 prefetch.2.10.7: 'SRR7444512' is valid 2020-06-25T23:26:24 prefetch.2.10.7: 1) 'SRR7444512' was downloaded successfully 2020-06-25T23:27:02 prefetch.2.10.7: 'SRR7444512' has 7 unresolved dependencies 2020-06-25T23:27:02 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.5?vdb-ctx=refseq'... 2020-06-25T23:27:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:33:06 prefetch.2.10.7: HTTPS download failed 2020-06-25T23:33:06 prefetch.2.10.7: 2) failed to download ncbi-acc:AE013599.5?vdb-ctx=refseq 2020-06-25T23:53:17 fastq-dump.2.10.7 err: transfer canceled while allocating buffer within file system module - Cannot KHttpFileTimedReadChunked: to=30 2020-06-25T23:53:17 fastq-dump.2.10.7 err: data corrupt while selecting function within transform module - failed SRR7444512/SRR7444512.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:22 7639040 reads; of these: 7639040 (100.00%) were unpaired; of these: 1207 (0.02%) aligned 0 times 6767570 (88.59%) aligned exactly 1 time 870263 (11.39%) aligned >1 times 99.98% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2263596 / 7637833 = 0.2964 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 08:58:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.bam'] # control file = None # effective genome size = 1.20e+08 # 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 08:58:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:58:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:58:43: 1000000 INFO @ Fri, 26 Jun 2020 08:58:51: 2000000 INFO @ Fri, 26 Jun 2020 08:58:59: 3000000 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 08:59:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.bam'] # control file = None # effective genome size = 1.20e+08 # 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 08:59:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:59:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:59:06: 4000000 INFO @ Fri, 26 Jun 2020 08:59:14: 1000000 INFO @ Fri, 26 Jun 2020 08:59:14: 5000000 INFO @ Fri, 26 Jun 2020 08:59:17: #1 tag size is determined as 75 bps INFO @ Fri, 26 Jun 2020 08:59:17: #1 tag size = 75 INFO @ Fri, 26 Jun 2020 08:59:17: #1 total tags in treatment: 5374237 INFO @ Fri, 26 Jun 2020 08:59:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:59:17: #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 08:59:17: #1 tags after filtering in treatment: 5374237 INFO @ Fri, 26 Jun 2020 08:59:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:59:17: #1 finished! INFO @ Fri, 26 Jun 2020 08:59:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:59:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:59:18: #2 number of paired peaks: 4363 INFO @ Fri, 26 Jun 2020 08:59:18: start model_add_line... INFO @ Fri, 26 Jun 2020 08:59:18: start X-correlation... INFO @ Fri, 26 Jun 2020 08:59:18: end of X-cor INFO @ Fri, 26 Jun 2020 08:59:18: #2 finished! INFO @ Fri, 26 Jun 2020 08:59:18: #2 predicted fragment length is 133 bps INFO @ Fri, 26 Jun 2020 08:59:18: #2 alternative fragment length(s) may be 133 bps INFO @ Fri, 26 Jun 2020 08:59:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.05_model.r WARNING @ Fri, 26 Jun 2020 08:59:18: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:59:18: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Fri, 26 Jun 2020 08:59:18: #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 08:59:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:59:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:59:21: 2000000 INFO @ Fri, 26 Jun 2020 08:59:28: 3000000 INFO @ Fri, 26 Jun 2020 08:59:33: #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 08:59:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.bam'] # control file = None # effective genome size = 1.20e+08 # 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 08:59:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:59:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:59:36: 4000000 INFO @ Fri, 26 Jun 2020 08:59:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:59:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:59:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.05_summits.bed INFO @ Fri, 26 Jun 2020 08:59:42: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (2076 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:59:44: 1000000 INFO @ Fri, 26 Jun 2020 08:59:44: 5000000 INFO @ Fri, 26 Jun 2020 08:59:47: #1 tag size is determined as 75 bps INFO @ Fri, 26 Jun 2020 08:59:47: #1 tag size = 75 INFO @ Fri, 26 Jun 2020 08:59:47: #1 total tags in treatment: 5374237 INFO @ Fri, 26 Jun 2020 08:59:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:59:47: #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 08:59:47: #1 tags after filtering in treatment: 5374237 INFO @ Fri, 26 Jun 2020 08:59:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:59:47: #1 finished! INFO @ Fri, 26 Jun 2020 08:59:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:59:47: #2 number of paired peaks: 4363 INFO @ Fri, 26 Jun 2020 08:59:47: start model_add_line... INFO @ Fri, 26 Jun 2020 08:59:47: start X-correlation... INFO @ Fri, 26 Jun 2020 08:59:47: end of X-cor INFO @ Fri, 26 Jun 2020 08:59:47: #2 finished! INFO @ Fri, 26 Jun 2020 08:59:47: #2 predicted fragment length is 133 bps INFO @ Fri, 26 Jun 2020 08:59:47: #2 alternative fragment length(s) may be 133 bps INFO @ Fri, 26 Jun 2020 08:59:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.10_model.r WARNING @ Fri, 26 Jun 2020 08:59:47: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:59:47: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Fri, 26 Jun 2020 08:59:47: #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 08:59:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:59:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:59:51: 2000000 INFO @ Fri, 26 Jun 2020 08:59:58: 3000000 INFO @ Fri, 26 Jun 2020 09:00:03: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:00:06: 4000000 INFO @ Fri, 26 Jun 2020 09:00:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:00:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:00:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.10_summits.bed INFO @ Fri, 26 Jun 2020 09:00:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (939 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:00:13: 5000000 INFO @ Fri, 26 Jun 2020 09:00:16: #1 tag size is determined as 75 bps INFO @ Fri, 26 Jun 2020 09:00:16: #1 tag size = 75 INFO @ Fri, 26 Jun 2020 09:00:16: #1 total tags in treatment: 5374237 INFO @ Fri, 26 Jun 2020 09:00:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:00:16: #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 09:00:16: #1 tags after filtering in treatment: 5374237 INFO @ Fri, 26 Jun 2020 09:00:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:00:16: #1 finished! INFO @ Fri, 26 Jun 2020 09:00:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:00:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:00:16: #2 number of paired peaks: 4363 INFO @ Fri, 26 Jun 2020 09:00:16: start model_add_line... INFO @ Fri, 26 Jun 2020 09:00:16: start X-correlation... INFO @ Fri, 26 Jun 2020 09:00:16: end of X-cor INFO @ Fri, 26 Jun 2020 09:00:16: #2 finished! INFO @ Fri, 26 Jun 2020 09:00:16: #2 predicted fragment length is 133 bps INFO @ Fri, 26 Jun 2020 09:00:16: #2 alternative fragment length(s) may be 133 bps INFO @ Fri, 26 Jun 2020 09:00:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.20_model.r WARNING @ Fri, 26 Jun 2020 09:00:16: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:00:16: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Fri, 26 Jun 2020 09:00:16: #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 09:00:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:00:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:00:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:00:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:00:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:00:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4315051/SRX4315051.20_summits.bed INFO @ Fri, 26 Jun 2020 09:00:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (366 records, 4 fields): 2 millis CompletedMACS2peakCalling