Job ID = 6508697 SRX = SRX4315051 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:47:39 prefetch.2.10.7: 1) Downloading 'SRR7444512'... 2020-06-26T14:47:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:49:04 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:49:05 prefetch.2.10.7: 'SRR7444512' is valid 2020-06-26T14:49:05 prefetch.2.10.7: 1) 'SRR7444512' was downloaded successfully 2020-06-26T14:49:43 prefetch.2.10.7: 'SRR7444512' has 7 unresolved dependencies 2020-06-26T14:49:43 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.5?vdb-ctx=refseq'... 2020-06-26T14:49:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:50:00 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:50:00 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.5?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:50:00 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.6?vdb-ctx=refseq'... 2020-06-26T14:50:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:50:17 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:50:17 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.6?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:50:17 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.4?vdb-ctx=refseq'... 2020-06-26T14:50:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:50:29 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:50:29 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:50:29 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.5?vdb-ctx=refseq'... 2020-06-26T14:50:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:50:46 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:50:46 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.5?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:50:46 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.3?vdb-ctx=refseq'... 2020-06-26T14:50:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:51:02 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:51:02 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:51:02 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.5?vdb-ctx=refseq'... 2020-06-26T14:51:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:51:19 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:51:19 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.5?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:51:19 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CP007106.1?vdb-ctx=refseq'... 2020-06-26T14:51:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:51:33 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:51:33 prefetch.2.10.7: 8) 'ncbi-acc:CP007106.1?vdb-ctx=refseq' was downloaded successfully Read 28179355 spots for SRR7444512/SRR7444512.sra Written 28179355 spots for SRR7444512/SRR7444512.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:46 28179355 reads; of these: 28179355 (100.00%) were unpaired; of these: 4791 (0.02%) aligned 0 times 25338444 (89.92%) aligned exactly 1 time 2836120 (10.06%) aligned >1 times 99.98% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 8645469 / 28174564 = 0.3069 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 @ Sat, 27 Jun 2020 00:08:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/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 @ Sat, 27 Jun 2020 00:08:14: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:08:14: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:08:21: 1000000 INFO @ Sat, 27 Jun 2020 00:08:28: 2000000 INFO @ Sat, 27 Jun 2020 00:08:34: 3000000 INFO @ Sat, 27 Jun 2020 00:08:41: 4000000 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 @ Sat, 27 Jun 2020 00:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/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 @ Sat, 27 Jun 2020 00:08:44: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:08:44: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:08:48: 5000000 INFO @ Sat, 27 Jun 2020 00:08:52: 1000000 INFO @ Sat, 27 Jun 2020 00:08:55: 6000000 INFO @ Sat, 27 Jun 2020 00:09:00: 2000000 INFO @ Sat, 27 Jun 2020 00:09:03: 7000000 INFO @ Sat, 27 Jun 2020 00:09:08: 3000000 INFO @ Sat, 27 Jun 2020 00:09:10: 8000000 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 @ Sat, 27 Jun 2020 00:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/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 @ Sat, 27 Jun 2020 00:09:14: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:09:14: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:09:17: 4000000 INFO @ Sat, 27 Jun 2020 00:09:18: 9000000 INFO @ Sat, 27 Jun 2020 00:09:22: 1000000 INFO @ Sat, 27 Jun 2020 00:09:25: 10000000 INFO @ Sat, 27 Jun 2020 00:09:26: 5000000 INFO @ Sat, 27 Jun 2020 00:09:31: 2000000 INFO @ Sat, 27 Jun 2020 00:09:33: 11000000 INFO @ Sat, 27 Jun 2020 00:09:34: 6000000 INFO @ Sat, 27 Jun 2020 00:09:39: 3000000 INFO @ Sat, 27 Jun 2020 00:09:41: 12000000 INFO @ Sat, 27 Jun 2020 00:09:43: 7000000 INFO @ Sat, 27 Jun 2020 00:09:48: 4000000 INFO @ Sat, 27 Jun 2020 00:09:48: 13000000 INFO @ Sat, 27 Jun 2020 00:09:52: 8000000 INFO @ Sat, 27 Jun 2020 00:09:56: 5000000 INFO @ Sat, 27 Jun 2020 00:09:56: 14000000 INFO @ Sat, 27 Jun 2020 00:10:00: 9000000 INFO @ Sat, 27 Jun 2020 00:10:04: 15000000 INFO @ Sat, 27 Jun 2020 00:10:04: 6000000 INFO @ Sat, 27 Jun 2020 00:10:09: 10000000 INFO @ Sat, 27 Jun 2020 00:10:12: 16000000 INFO @ Sat, 27 Jun 2020 00:10:13: 7000000 INFO @ Sat, 27 Jun 2020 00:10:17: 11000000 INFO @ Sat, 27 Jun 2020 00:10:19: 17000000 INFO @ Sat, 27 Jun 2020 00:10:21: 8000000 INFO @ Sat, 27 Jun 2020 00:10:25: 12000000 INFO @ Sat, 27 Jun 2020 00:10:27: 18000000 INFO @ Sat, 27 Jun 2020 00:10:30: 9000000 INFO @ Sat, 27 Jun 2020 00:10:34: 13000000 INFO @ Sat, 27 Jun 2020 00:10:34: 19000000 INFO @ Sat, 27 Jun 2020 00:10:38: 10000000 INFO @ Sat, 27 Jun 2020 00:10:39: #1 tag size is determined as 75 bps INFO @ Sat, 27 Jun 2020 00:10:39: #1 tag size = 75 INFO @ Sat, 27 Jun 2020 00:10:39: #1 total tags in treatment: 19529095 INFO @ Sat, 27 Jun 2020 00:10:39: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:10:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:10:39: #1 tags after filtering in treatment: 19528966 INFO @ Sat, 27 Jun 2020 00:10:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:10:39: #1 finished! INFO @ Sat, 27 Jun 2020 00:10:39: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:10:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:10:41: #2 number of paired peaks: 160 WARNING @ Sat, 27 Jun 2020 00:10:41: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sat, 27 Jun 2020 00:10:41: start model_add_line... INFO @ Sat, 27 Jun 2020 00:10:41: start X-correlation... INFO @ Sat, 27 Jun 2020 00:10:41: end of X-cor INFO @ Sat, 27 Jun 2020 00:10:41: #2 finished! INFO @ Sat, 27 Jun 2020 00:10:41: #2 predicted fragment length is 89 bps INFO @ Sat, 27 Jun 2020 00:10:41: #2 alternative fragment length(s) may be 4,89,102 bps INFO @ Sat, 27 Jun 2020 00:10:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.05_model.r WARNING @ Sat, 27 Jun 2020 00:10:41: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:10:41: #2 You may need to consider one of the other alternative d(s): 4,89,102 WARNING @ Sat, 27 Jun 2020 00:10:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:10:41: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:10:42: 14000000 INFO @ Sat, 27 Jun 2020 00:10:47: 11000000 INFO @ Sat, 27 Jun 2020 00:10:50: 15000000 INFO @ Sat, 27 Jun 2020 00:10:55: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:10:59: 16000000 INFO @ Sat, 27 Jun 2020 00:11:03: 13000000 INFO @ Sat, 27 Jun 2020 00:11:07: 17000000 INFO @ Sat, 27 Jun 2020 00:11:11: 14000000 INFO @ Sat, 27 Jun 2020 00:11:15: 18000000 INFO @ Sat, 27 Jun 2020 00:11:19: 15000000 INFO @ Sat, 27 Jun 2020 00:11:23: 19000000 INFO @ Sat, 27 Jun 2020 00:11:27: 16000000 INFO @ Sat, 27 Jun 2020 00:11:27: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:11:28: #1 tag size is determined as 75 bps INFO @ Sat, 27 Jun 2020 00:11:28: #1 tag size = 75 INFO @ Sat, 27 Jun 2020 00:11:28: #1 total tags in treatment: 19529095 INFO @ Sat, 27 Jun 2020 00:11:28: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:11:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:11:28: #1 tags after filtering in treatment: 19528966 INFO @ Sat, 27 Jun 2020 00:11:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:11:28: #1 finished! INFO @ Sat, 27 Jun 2020 00:11:28: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:11:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:11:29: #2 number of paired peaks: 160 WARNING @ Sat, 27 Jun 2020 00:11:29: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sat, 27 Jun 2020 00:11:29: start model_add_line... INFO @ Sat, 27 Jun 2020 00:11:30: start X-correlation... INFO @ Sat, 27 Jun 2020 00:11:30: end of X-cor INFO @ Sat, 27 Jun 2020 00:11:30: #2 finished! INFO @ Sat, 27 Jun 2020 00:11:30: #2 predicted fragment length is 89 bps INFO @ Sat, 27 Jun 2020 00:11:30: #2 alternative fragment length(s) may be 4,89,102 bps INFO @ Sat, 27 Jun 2020 00:11:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.10_model.r WARNING @ Sat, 27 Jun 2020 00:11:30: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:11:30: #2 You may need to consider one of the other alternative d(s): 4,89,102 WARNING @ Sat, 27 Jun 2020 00:11:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:11:30: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:11:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:11:34: 17000000 INFO @ Sat, 27 Jun 2020 00:11:41: 18000000 BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:11:48: 19000000 INFO @ Sat, 27 Jun 2020 00:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.05_summits.bed INFO @ Sat, 27 Jun 2020 00:11:50: Done! pass1 - making usageList (132 chroms): 2 millis pass2 - checking and writing primary data (5650 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:11:52: #1 tag size is determined as 75 bps INFO @ Sat, 27 Jun 2020 00:11:52: #1 tag size = 75 INFO @ Sat, 27 Jun 2020 00:11:52: #1 total tags in treatment: 19529095 INFO @ Sat, 27 Jun 2020 00:11:52: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:11:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:11:53: #1 tags after filtering in treatment: 19528966 INFO @ Sat, 27 Jun 2020 00:11:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:11:53: #1 finished! INFO @ Sat, 27 Jun 2020 00:11:53: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:11:54: #2 number of paired peaks: 160 WARNING @ Sat, 27 Jun 2020 00:11:54: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sat, 27 Jun 2020 00:11:54: start model_add_line... INFO @ Sat, 27 Jun 2020 00:11:54: start X-correlation... INFO @ Sat, 27 Jun 2020 00:11:54: end of X-cor INFO @ Sat, 27 Jun 2020 00:11:54: #2 finished! INFO @ Sat, 27 Jun 2020 00:11:54: #2 predicted fragment length is 89 bps INFO @ Sat, 27 Jun 2020 00:11:54: #2 alternative fragment length(s) may be 4,89,102 bps INFO @ Sat, 27 Jun 2020 00:11:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.20_model.r WARNING @ Sat, 27 Jun 2020 00:11:54: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:11:54: #2 You may need to consider one of the other alternative d(s): 4,89,102 WARNING @ Sat, 27 Jun 2020 00:11:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:11:54: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:11:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:12:11: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:12:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:12:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:12:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.10_summits.bed INFO @ Sat, 27 Jun 2020 00:12:32: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (3031 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:12:35: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:12:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:12:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:12:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315051/SRX4315051.20_summits.bed INFO @ Sat, 27 Jun 2020 00:12:54: Done! pass1 - making usageList (72 chroms): 1 millis pass2 - checking and writing primary data (1259 records, 4 fields): 5 millis CompletedMACS2peakCalling