Job ID = 6451783 SRX = ERX011408 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:32:12 prefetch.2.10.7: 1) Downloading 'ERR031129'... 2020-06-21T07:32:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:33:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:33:44 prefetch.2.10.7: 'ERR031129' is valid 2020-06-21T07:33:44 prefetch.2.10.7: 1) 'ERR031129' was downloaded successfully 2020-06-21T07:34:37 prefetch.2.10.7: 'ERR031129' has 10 unresolved dependencies 2020-06-21T07:34:37 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T07:34:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:34:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:34:54 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:34:54 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T07:34:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:35:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:35:12 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:35:12 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T07:35:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:35:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:35:24 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:35:24 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T07:35:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:35:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:35:41 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:35:41 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T07:35:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:35:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:35:58 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:35:58 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T07:35:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:36:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:36:16 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:36:16 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T07:36:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:36:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:36:29 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:36:29 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T07:36:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:36:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:36:42 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:36:42 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T07:36:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:36:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:36:54 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:36:54 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T07:36:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:37:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:37:09 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 23462340 spots for ERR031129/ERR031129.sra Written 23462340 spots for ERR031129/ERR031129.sra 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: 00:04:33 23462340 reads; of these: 23462340 (100.00%) were unpaired; of these: 760982 (3.24%) aligned 0 times 16767593 (71.47%) aligned exactly 1 time 5933765 (25.29%) aligned >1 times 96.76% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6197093 / 22701358 = 0.2730 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 @ Sun, 21 Jun 2020 16:46:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.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 @ Sun, 21 Jun 2020 16:46:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:46:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:46:59: 1000000 INFO @ Sun, 21 Jun 2020 16:47:05: 2000000 INFO @ Sun, 21 Jun 2020 16:47:10: 3000000 INFO @ Sun, 21 Jun 2020 16:47:16: 4000000 INFO @ Sun, 21 Jun 2020 16:47:22: 5000000 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 @ Sun, 21 Jun 2020 16:47:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.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 @ Sun, 21 Jun 2020 16:47:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:47:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:47:27: 6000000 INFO @ Sun, 21 Jun 2020 16:47:30: 1000000 INFO @ Sun, 21 Jun 2020 16:47:33: 7000000 INFO @ Sun, 21 Jun 2020 16:47:36: 2000000 INFO @ Sun, 21 Jun 2020 16:47:39: 8000000 INFO @ Sun, 21 Jun 2020 16:47:42: 3000000 INFO @ Sun, 21 Jun 2020 16:47:45: 9000000 INFO @ Sun, 21 Jun 2020 16:47:48: 4000000 INFO @ Sun, 21 Jun 2020 16:47:51: 10000000 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 @ Sun, 21 Jun 2020 16:47:54: 5000000 INFO @ Sun, 21 Jun 2020 16:47:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.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 @ Sun, 21 Jun 2020 16:47:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:47:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:47:57: 11000000 INFO @ Sun, 21 Jun 2020 16:48:00: 1000000 INFO @ Sun, 21 Jun 2020 16:48:00: 6000000 INFO @ Sun, 21 Jun 2020 16:48:03: 12000000 INFO @ Sun, 21 Jun 2020 16:48:06: 2000000 INFO @ Sun, 21 Jun 2020 16:48:06: 7000000 INFO @ Sun, 21 Jun 2020 16:48:09: 13000000 INFO @ Sun, 21 Jun 2020 16:48:12: 3000000 INFO @ Sun, 21 Jun 2020 16:48:12: 8000000 INFO @ Sun, 21 Jun 2020 16:48:15: 14000000 INFO @ Sun, 21 Jun 2020 16:48:18: 4000000 INFO @ Sun, 21 Jun 2020 16:48:19: 9000000 INFO @ Sun, 21 Jun 2020 16:48:21: 15000000 INFO @ Sun, 21 Jun 2020 16:48:24: 5000000 INFO @ Sun, 21 Jun 2020 16:48:25: 10000000 INFO @ Sun, 21 Jun 2020 16:48:27: 16000000 INFO @ Sun, 21 Jun 2020 16:48:30: 6000000 INFO @ Sun, 21 Jun 2020 16:48:31: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:48:31: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:48:31: #1 total tags in treatment: 16504265 INFO @ Sun, 21 Jun 2020 16:48:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:48:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:48:31: 11000000 INFO @ Sun, 21 Jun 2020 16:48:31: #1 tags after filtering in treatment: 16504262 INFO @ Sun, 21 Jun 2020 16:48:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:48:31: #1 finished! INFO @ Sun, 21 Jun 2020 16:48:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:48:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:48:32: #2 number of paired peaks: 656 WARNING @ Sun, 21 Jun 2020 16:48:32: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Sun, 21 Jun 2020 16:48:32: start model_add_line... INFO @ Sun, 21 Jun 2020 16:48:32: start X-correlation... INFO @ Sun, 21 Jun 2020 16:48:32: end of X-cor INFO @ Sun, 21 Jun 2020 16:48:32: #2 finished! INFO @ Sun, 21 Jun 2020 16:48:32: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 16:48:32: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 16:48:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.05_model.r WARNING @ Sun, 21 Jun 2020 16:48:32: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:48:32: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 16:48:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:48:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:48:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:48:36: 7000000 INFO @ Sun, 21 Jun 2020 16:48:37: 12000000 INFO @ Sun, 21 Jun 2020 16:48:42: 8000000 INFO @ Sun, 21 Jun 2020 16:48:43: 13000000 INFO @ Sun, 21 Jun 2020 16:48:48: 9000000 INFO @ Sun, 21 Jun 2020 16:48:49: 14000000 INFO @ Sun, 21 Jun 2020 16:48:54: 10000000 INFO @ Sun, 21 Jun 2020 16:48:55: 15000000 INFO @ Sun, 21 Jun 2020 16:49:00: 11000000 INFO @ Sun, 21 Jun 2020 16:49:02: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:49:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:49:05: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:49:05: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:49:05: #1 total tags in treatment: 16504265 INFO @ Sun, 21 Jun 2020 16:49:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:49:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:49:05: #1 tags after filtering in treatment: 16504262 INFO @ Sun, 21 Jun 2020 16:49:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:49:05: #1 finished! INFO @ Sun, 21 Jun 2020 16:49:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:49:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:49:06: 12000000 INFO @ Sun, 21 Jun 2020 16:49:06: #2 number of paired peaks: 656 WARNING @ Sun, 21 Jun 2020 16:49:06: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Sun, 21 Jun 2020 16:49:06: start model_add_line... INFO @ Sun, 21 Jun 2020 16:49:06: start X-correlation... INFO @ Sun, 21 Jun 2020 16:49:06: end of X-cor INFO @ Sun, 21 Jun 2020 16:49:06: #2 finished! INFO @ Sun, 21 Jun 2020 16:49:06: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 16:49:06: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 16:49:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.10_model.r WARNING @ Sun, 21 Jun 2020 16:49:06: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:49:06: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 16:49:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:49:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:49:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:49:12: 13000000 INFO @ Sun, 21 Jun 2020 16:49:17: 14000000 INFO @ Sun, 21 Jun 2020 16:49:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:49:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:49:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.05_summits.bed INFO @ Sun, 21 Jun 2020 16:49:18: Done! pass1 - making usageList (699 chroms): 1 millis pass2 - checking and writing primary data (3494 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:49:23: 15000000 INFO @ Sun, 21 Jun 2020 16:49:29: 16000000 INFO @ Sun, 21 Jun 2020 16:49:31: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:49:31: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:49:31: #1 total tags in treatment: 16504265 INFO @ Sun, 21 Jun 2020 16:49:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:49:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:49:32: #1 tags after filtering in treatment: 16504262 INFO @ Sun, 21 Jun 2020 16:49:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:49:32: #1 finished! INFO @ Sun, 21 Jun 2020 16:49:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:49:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:49:33: #2 number of paired peaks: 656 WARNING @ Sun, 21 Jun 2020 16:49:33: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Sun, 21 Jun 2020 16:49:33: start model_add_line... INFO @ Sun, 21 Jun 2020 16:49:33: start X-correlation... INFO @ Sun, 21 Jun 2020 16:49:33: end of X-cor INFO @ Sun, 21 Jun 2020 16:49:33: #2 finished! INFO @ Sun, 21 Jun 2020 16:49:33: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 16:49:33: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 16:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.20_model.r WARNING @ Sun, 21 Jun 2020 16:49:33: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:49:33: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 16:49:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:49:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:49:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:49:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:49:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:49:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.10_summits.bed INFO @ Sun, 21 Jun 2020 16:49:51: Done! pass1 - making usageList (406 chroms): 1 millis pass2 - checking and writing primary data (1350 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:50:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:50:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:50:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:50:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011408/ERX011408.20_summits.bed INFO @ Sun, 21 Jun 2020 16:50:20: Done! pass1 - making usageList (212 chroms): 1 millis pass2 - checking and writing primary data (584 records, 4 fields): 7 millis CompletedMACS2peakCalling