Job ID = 6457554 SRX = SRX4669043 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:44:48 prefetch.2.10.7: 1) Downloading 'SRR7817568'... 2020-06-21T11:44:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:47:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:47:29 prefetch.2.10.7: 'SRR7817568' is valid 2020-06-21T11:47:29 prefetch.2.10.7: 1) 'SRR7817568' was downloaded successfully 2020-06-21T11:47:29 prefetch.2.10.7: 'SRR7817568' has 0 unresolved dependencies Read 27535452 spots for SRR7817568/SRR7817568.sra Written 27535452 spots for SRR7817568/SRR7817568.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: 00:07:09 27535452 reads; of these: 27535452 (100.00%) were unpaired; of these: 2696447 (9.79%) aligned 0 times 17503274 (63.57%) aligned exactly 1 time 7335731 (26.64%) aligned >1 times 90.21% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 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] 9713309 / 24839005 = 0.3911 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 21:00:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.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 21:00:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:00:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:00:39: 1000000 INFO @ Sun, 21 Jun 2020 21:00:44: 2000000 INFO @ Sun, 21 Jun 2020 21:00:50: 3000000 INFO @ Sun, 21 Jun 2020 21:00:55: 4000000 INFO @ Sun, 21 Jun 2020 21:01:01: 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 21:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.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 21:01:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:01:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:01:06: 6000000 INFO @ Sun, 21 Jun 2020 21:01:09: 1000000 INFO @ Sun, 21 Jun 2020 21:01:12: 7000000 INFO @ Sun, 21 Jun 2020 21:01:15: 2000000 INFO @ Sun, 21 Jun 2020 21:01:17: 8000000 INFO @ Sun, 21 Jun 2020 21:01:20: 3000000 INFO @ Sun, 21 Jun 2020 21:01:23: 9000000 INFO @ Sun, 21 Jun 2020 21:01:26: 4000000 INFO @ Sun, 21 Jun 2020 21:01:28: 10000000 INFO @ Sun, 21 Jun 2020 21:01:31: 5000000 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 21:01:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.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 21:01:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:01:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:01:34: 11000000 INFO @ Sun, 21 Jun 2020 21:01:37: 6000000 INFO @ Sun, 21 Jun 2020 21:01:39: 1000000 INFO @ Sun, 21 Jun 2020 21:01:40: 12000000 INFO @ Sun, 21 Jun 2020 21:01:43: 7000000 INFO @ Sun, 21 Jun 2020 21:01:45: 2000000 INFO @ Sun, 21 Jun 2020 21:01:45: 13000000 INFO @ Sun, 21 Jun 2020 21:01:48: 8000000 INFO @ Sun, 21 Jun 2020 21:01:50: 3000000 INFO @ Sun, 21 Jun 2020 21:01:51: 14000000 INFO @ Sun, 21 Jun 2020 21:01:53: 9000000 INFO @ Sun, 21 Jun 2020 21:01:56: 4000000 INFO @ Sun, 21 Jun 2020 21:01:57: 15000000 INFO @ Sun, 21 Jun 2020 21:01:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:01:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:01:58: #1 total tags in treatment: 15125696 INFO @ Sun, 21 Jun 2020 21:01:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:01:58: #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 21:01:58: #1 tags after filtering in treatment: 15125695 INFO @ Sun, 21 Jun 2020 21:01:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:01:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:01:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:01:59: 10000000 INFO @ Sun, 21 Jun 2020 21:01:59: #2 number of paired peaks: 1841 INFO @ Sun, 21 Jun 2020 21:01:59: start model_add_line... INFO @ Sun, 21 Jun 2020 21:01:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:01:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:01:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:01:59: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 21:01:59: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 21:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.05_model.r INFO @ Sun, 21 Jun 2020 21:01:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:01:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:02:01: 5000000 INFO @ Sun, 21 Jun 2020 21:02:04: 11000000 INFO @ Sun, 21 Jun 2020 21:02:07: 6000000 INFO @ Sun, 21 Jun 2020 21:02:10: 12000000 INFO @ Sun, 21 Jun 2020 21:02:13: 7000000 INFO @ Sun, 21 Jun 2020 21:02:15: 13000000 INFO @ Sun, 21 Jun 2020 21:02:18: 8000000 INFO @ Sun, 21 Jun 2020 21:02:21: 14000000 INFO @ Sun, 21 Jun 2020 21:02:24: 9000000 INFO @ Sun, 21 Jun 2020 21:02:26: 15000000 INFO @ Sun, 21 Jun 2020 21:02:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:02:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:02:27: #1 total tags in treatment: 15125696 INFO @ Sun, 21 Jun 2020 21:02:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:27: #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 21:02:28: #1 tags after filtering in treatment: 15125695 INFO @ Sun, 21 Jun 2020 21:02:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:29: 10000000 INFO @ Sun, 21 Jun 2020 21:02:29: #2 number of paired peaks: 1841 INFO @ Sun, 21 Jun 2020 21:02:29: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:29: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:29: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:29: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:29: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 21:02:29: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 21:02:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.10_model.r INFO @ Sun, 21 Jun 2020 21:02:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:02:34: 11000000 INFO @ Sun, 21 Jun 2020 21:02:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:02:39: 12000000 INFO @ Sun, 21 Jun 2020 21:02:44: 13000000 INFO @ Sun, 21 Jun 2020 21:02:50: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:02:55: 15000000 INFO @ Sun, 21 Jun 2020 21:02:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:02:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:02:56: #1 total tags in treatment: 15125696 INFO @ Sun, 21 Jun 2020 21:02:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:56: #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 21:02:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:02:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:02:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.05_summits.bed INFO @ Sun, 21 Jun 2020 21:02:56: #1 tags after filtering in treatment: 15125695 INFO @ Sun, 21 Jun 2020 21:02:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:56: Done! pass1 - making usageList (750 chroms): 2 millis pass2 - checking and writing primary data (9211 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:02:57: #2 number of paired peaks: 1841 INFO @ Sun, 21 Jun 2020 21:02:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:58: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 21:02:58: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 21:02:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.20_model.r INFO @ Sun, 21 Jun 2020 21:02:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:03:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:03:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:03:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:03:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.10_summits.bed INFO @ Sun, 21 Jun 2020 21:03:24: Done! pass1 - making usageList (622 chroms): 1 millis pass2 - checking and writing primary data (5476 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:03:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:03:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:03:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:03:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669043/SRX4669043.20_summits.bed INFO @ Sun, 21 Jun 2020 21:03:54: Done! pass1 - making usageList (439 chroms): 1 millis pass2 - checking and writing primary data (2757 records, 4 fields): 25 millis CompletedMACS2peakCalling