Job ID = 6457027 SRX = SRX4315049 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:18:57 prefetch.2.10.7: 1) Downloading 'SRR7444510'... 2020-06-21T11:18:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:21:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:21:50 prefetch.2.10.7: 'SRR7444510' is valid 2020-06-21T11:21:50 prefetch.2.10.7: 1) 'SRR7444510' was downloaded successfully 2020-06-21T11:22:27 prefetch.2.10.7: 'SRR7444510' has 7 unresolved dependencies 2020-06-21T11:22:27 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.5?vdb-ctx=refseq'... 2020-06-21T11:22:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:44 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:22:44 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.6?vdb-ctx=refseq'... 2020-06-21T11:22:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:23:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:23:01 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.6?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:23:01 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.4?vdb-ctx=refseq'... 2020-06-21T11:23:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:23:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:23:14 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:23:14 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.5?vdb-ctx=refseq'... 2020-06-21T11:23:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:23:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:23:31 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:23:31 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.3?vdb-ctx=refseq'... 2020-06-21T11:23:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:23:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:23:47 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:23:47 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.5?vdb-ctx=refseq'... 2020-06-21T11:23:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:24:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:24:04 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:24:04 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CP007106.1?vdb-ctx=refseq'... 2020-06-21T11:24:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:24:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:24:17 prefetch.2.10.7: 8) 'ncbi-acc:CP007106.1?vdb-ctx=refseq' was downloaded successfully Read 33635931 spots for SRR7444510/SRR7444510.sra Written 33635931 spots for SRR7444510/SRR7444510.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: 00:06:03 33635931 reads; of these: 33635931 (100.00%) were unpaired; of these: 3401 (0.01%) aligned 0 times 31693651 (94.23%) aligned exactly 1 time 1938879 (5.76%) aligned >1 times 99.99% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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 16 files... [bam_rmdupse_core] 8993973 / 33632530 = 0.2674 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 20:40:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.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 20:40:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:24: 1000000 INFO @ Sun, 21 Jun 2020 20:40:30: 2000000 INFO @ Sun, 21 Jun 2020 20:40:37: 3000000 INFO @ Sun, 21 Jun 2020 20:40:44: 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 @ Sun, 21 Jun 2020 20:40:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.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 20:40:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:51: 5000000 INFO @ Sun, 21 Jun 2020 20:40:55: 1000000 INFO @ Sun, 21 Jun 2020 20:40:58: 6000000 INFO @ Sun, 21 Jun 2020 20:41:03: 2000000 INFO @ Sun, 21 Jun 2020 20:41:06: 7000000 INFO @ Sun, 21 Jun 2020 20:41:11: 3000000 INFO @ Sun, 21 Jun 2020 20:41:14: 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 @ Sun, 21 Jun 2020 20:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.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 20:41:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:41:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:41:19: 4000000 INFO @ Sun, 21 Jun 2020 20:41:22: 9000000 INFO @ Sun, 21 Jun 2020 20:41:27: 1000000 INFO @ Sun, 21 Jun 2020 20:41:29: 5000000 INFO @ Sun, 21 Jun 2020 20:41:31: 10000000 INFO @ Sun, 21 Jun 2020 20:41:36: 2000000 INFO @ Sun, 21 Jun 2020 20:41:38: 6000000 INFO @ Sun, 21 Jun 2020 20:41:39: 11000000 INFO @ Sun, 21 Jun 2020 20:41:46: 3000000 INFO @ Sun, 21 Jun 2020 20:41:47: 7000000 INFO @ Sun, 21 Jun 2020 20:41:48: 12000000 INFO @ Sun, 21 Jun 2020 20:41:55: 4000000 INFO @ Sun, 21 Jun 2020 20:41:56: 8000000 INFO @ Sun, 21 Jun 2020 20:41:57: 13000000 INFO @ Sun, 21 Jun 2020 20:42:04: 5000000 INFO @ Sun, 21 Jun 2020 20:42:05: 9000000 INFO @ Sun, 21 Jun 2020 20:42:05: 14000000 INFO @ Sun, 21 Jun 2020 20:42:13: 6000000 INFO @ Sun, 21 Jun 2020 20:42:14: 15000000 INFO @ Sun, 21 Jun 2020 20:42:14: 10000000 INFO @ Sun, 21 Jun 2020 20:42:22: 16000000 INFO @ Sun, 21 Jun 2020 20:42:23: 7000000 INFO @ Sun, 21 Jun 2020 20:42:23: 11000000 INFO @ Sun, 21 Jun 2020 20:42:31: 17000000 INFO @ Sun, 21 Jun 2020 20:42:32: 8000000 INFO @ Sun, 21 Jun 2020 20:42:32: 12000000 INFO @ Sun, 21 Jun 2020 20:42:39: 18000000 INFO @ Sun, 21 Jun 2020 20:42:41: 9000000 INFO @ Sun, 21 Jun 2020 20:42:41: 13000000 INFO @ Sun, 21 Jun 2020 20:42:48: 19000000 INFO @ Sun, 21 Jun 2020 20:42:50: 10000000 INFO @ Sun, 21 Jun 2020 20:42:50: 14000000 INFO @ Sun, 21 Jun 2020 20:42:57: 20000000 INFO @ Sun, 21 Jun 2020 20:42:59: 11000000 INFO @ Sun, 21 Jun 2020 20:42:59: 15000000 INFO @ Sun, 21 Jun 2020 20:43:05: 21000000 INFO @ Sun, 21 Jun 2020 20:43:08: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:43:08: 16000000 INFO @ Sun, 21 Jun 2020 20:43:14: 22000000 INFO @ Sun, 21 Jun 2020 20:43:17: 17000000 INFO @ Sun, 21 Jun 2020 20:43:17: 13000000 INFO @ Sun, 21 Jun 2020 20:43:23: 23000000 INFO @ Sun, 21 Jun 2020 20:43:26: 18000000 INFO @ Sun, 21 Jun 2020 20:43:27: 14000000 INFO @ Sun, 21 Jun 2020 20:43:31: 24000000 INFO @ Sun, 21 Jun 2020 20:43:35: 19000000 INFO @ Sun, 21 Jun 2020 20:43:36: 15000000 INFO @ Sun, 21 Jun 2020 20:43:37: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:43:37: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:43:37: #1 total tags in treatment: 24638557 INFO @ Sun, 21 Jun 2020 20:43:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:37: #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 20:43:38: #1 tags after filtering in treatment: 24638406 INFO @ Sun, 21 Jun 2020 20:43:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:38: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:40: #2 number of paired peaks: 9527 INFO @ Sun, 21 Jun 2020 20:43:40: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:41: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 20:43:41: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 20:43:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.05_model.r WARNING @ Sun, 21 Jun 2020 20:43:41: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:43:41: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 20:43:41: #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 20:43:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:43:44: 20000000 INFO @ Sun, 21 Jun 2020 20:43:46: 16000000 INFO @ Sun, 21 Jun 2020 20:43:53: 21000000 INFO @ Sun, 21 Jun 2020 20:43:55: 17000000 INFO @ Sun, 21 Jun 2020 20:44:02: 22000000 INFO @ Sun, 21 Jun 2020 20:44:04: 18000000 INFO @ Sun, 21 Jun 2020 20:44:11: 23000000 INFO @ Sun, 21 Jun 2020 20:44:14: 19000000 INFO @ Sun, 21 Jun 2020 20:44:20: 24000000 INFO @ Sun, 21 Jun 2020 20:44:24: 20000000 INFO @ Sun, 21 Jun 2020 20:44:26: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:44:26: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:44:26: #1 total tags in treatment: 24638557 INFO @ Sun, 21 Jun 2020 20:44:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:26: #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 20:44:26: #1 tags after filtering in treatment: 24638406 INFO @ Sun, 21 Jun 2020 20:44:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:26: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:29: #2 number of paired peaks: 9527 INFO @ Sun, 21 Jun 2020 20:44:29: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:29: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:29: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:29: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:29: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 20:44:29: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 20:44:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.10_model.r WARNING @ Sun, 21 Jun 2020 20:44:29: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:44:29: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 20:44:29: #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 20:44:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:44:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:33: 21000000 INFO @ Sun, 21 Jun 2020 20:44:41: 22000000 INFO @ Sun, 21 Jun 2020 20:44:50: 23000000 INFO @ Sun, 21 Jun 2020 20:44:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.05_summits.bed INFO @ Sun, 21 Jun 2020 20:44:56: Done! pass1 - making usageList (89 chroms): 2 millis pass2 - checking and writing primary data (11712 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:44:58: 24000000 INFO @ Sun, 21 Jun 2020 20:45:04: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:45:04: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:45:04: #1 total tags in treatment: 24638557 INFO @ Sun, 21 Jun 2020 20:45:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:45:04: #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 20:45:04: #1 tags after filtering in treatment: 24638406 INFO @ Sun, 21 Jun 2020 20:45:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:45:04: #1 finished! INFO @ Sun, 21 Jun 2020 20:45:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:45:07: #2 number of paired peaks: 9527 INFO @ Sun, 21 Jun 2020 20:45:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:45:07: start X-correlation... INFO @ Sun, 21 Jun 2020 20:45:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:45:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:45:07: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 20:45:07: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 20:45:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.20_model.r WARNING @ Sun, 21 Jun 2020 20:45:07: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:45:07: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 20:45:07: #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 20:45:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:45:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:45:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.10_summits.bed INFO @ Sun, 21 Jun 2020 20:45:43: Done! pass1 - making usageList (62 chroms): 2 millis pass2 - checking and writing primary data (9903 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:45:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:46:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:46:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:46:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315049/SRX4315049.20_summits.bed INFO @ Sun, 21 Jun 2020 20:46:20: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (7711 records, 4 fields): 8 millis CompletedMACS2peakCalling