Job ID = 6454621 SRX = SRX2417578 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:15:24 prefetch.2.10.7: 1) Downloading 'SRR5101090'... 2020-06-21T09:15:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:18:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:18:52 prefetch.2.10.7: 'SRR5101090' is valid 2020-06-21T09:18:52 prefetch.2.10.7: 1) 'SRR5101090' was downloaded successfully Read 19310617 spots for SRR5101090/SRR5101090.sra Written 19310617 spots for SRR5101090/SRR5101090.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: 00:07:29 19310617 reads; of these: 19310617 (100.00%) were unpaired; of these: 573198 (2.97%) aligned 0 times 8482624 (43.93%) aligned exactly 1 time 10254795 (53.10%) aligned >1 times 97.03% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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] 4314016 / 18737419 = 0.2302 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 18:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.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 18:31:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:16: 1000000 INFO @ Sun, 21 Jun 2020 18:31:23: 2000000 INFO @ Sun, 21 Jun 2020 18:31:29: 3000000 INFO @ Sun, 21 Jun 2020 18:31:36: 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 18:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.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 18:31:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:43: 5000000 INFO @ Sun, 21 Jun 2020 18:31:47: 1000000 INFO @ Sun, 21 Jun 2020 18:31:51: 6000000 INFO @ Sun, 21 Jun 2020 18:31:53: 2000000 INFO @ Sun, 21 Jun 2020 18:31:58: 7000000 INFO @ Sun, 21 Jun 2020 18:32:00: 3000000 INFO @ Sun, 21 Jun 2020 18:32:06: 8000000 INFO @ Sun, 21 Jun 2020 18:32:07: 4000000 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 18:32:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.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 18:32:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:13: 9000000 INFO @ Sun, 21 Jun 2020 18:32:13: 5000000 INFO @ Sun, 21 Jun 2020 18:32:17: 1000000 INFO @ Sun, 21 Jun 2020 18:32:20: 6000000 INFO @ Sun, 21 Jun 2020 18:32:21: 10000000 INFO @ Sun, 21 Jun 2020 18:32:23: 2000000 INFO @ Sun, 21 Jun 2020 18:32:27: 7000000 INFO @ Sun, 21 Jun 2020 18:32:28: 11000000 INFO @ Sun, 21 Jun 2020 18:32:30: 3000000 INFO @ Sun, 21 Jun 2020 18:32:35: 8000000 INFO @ Sun, 21 Jun 2020 18:32:36: 12000000 INFO @ Sun, 21 Jun 2020 18:32:37: 4000000 INFO @ Sun, 21 Jun 2020 18:32:41: 9000000 INFO @ Sun, 21 Jun 2020 18:32:44: 13000000 INFO @ Sun, 21 Jun 2020 18:32:44: 5000000 INFO @ Sun, 21 Jun 2020 18:32:48: 10000000 INFO @ Sun, 21 Jun 2020 18:32:51: 14000000 INFO @ Sun, 21 Jun 2020 18:32:52: 6000000 INFO @ Sun, 21 Jun 2020 18:32:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:32:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:32:54: #1 total tags in treatment: 14423403 INFO @ Sun, 21 Jun 2020 18:32:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:54: #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 18:32:55: #1 tags after filtering in treatment: 14423345 INFO @ Sun, 21 Jun 2020 18:32:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:55: 11000000 INFO @ Sun, 21 Jun 2020 18:32:56: #2 number of paired peaks: 2577 INFO @ Sun, 21 Jun 2020 18:32:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:56: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:32:56: #2 alternative fragment length(s) may be 2,52 bps INFO @ Sun, 21 Jun 2020 18:32:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.05_model.r WARNING @ Sun, 21 Jun 2020 18:32:56: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:32:56: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Sun, 21 Jun 2020 18:32:56: #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 18:32:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:59: 7000000 INFO @ Sun, 21 Jun 2020 18:33:02: 12000000 INFO @ Sun, 21 Jun 2020 18:33:06: 8000000 INFO @ Sun, 21 Jun 2020 18:33:09: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:33:12: 9000000 INFO @ Sun, 21 Jun 2020 18:33:16: 14000000 INFO @ Sun, 21 Jun 2020 18:33:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:18: #1 total tags in treatment: 14423403 INFO @ Sun, 21 Jun 2020 18:33:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:18: #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 18:33:19: 10000000 INFO @ Sun, 21 Jun 2020 18:33:19: #1 tags after filtering in treatment: 14423345 INFO @ Sun, 21 Jun 2020 18:33:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:20: #2 number of paired peaks: 2577 INFO @ Sun, 21 Jun 2020 18:33:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:20: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:33:20: #2 alternative fragment length(s) may be 2,52 bps INFO @ Sun, 21 Jun 2020 18:33:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.10_model.r WARNING @ Sun, 21 Jun 2020 18:33:20: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:20: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Sun, 21 Jun 2020 18:33:20: #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 18:33:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:25: 11000000 INFO @ Sun, 21 Jun 2020 18:33:31: 12000000 INFO @ Sun, 21 Jun 2020 18:33:36: 13000000 INFO @ Sun, 21 Jun 2020 18:33:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.05_summits.bed INFO @ Sun, 21 Jun 2020 18:33:37: Done! BigWig に変換しました。 pass1 - making usageList (924 chroms): 2 millis pass2 - checking and writing primary data (5408 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:33:42: 14000000 INFO @ Sun, 21 Jun 2020 18:33:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:44: #1 total tags in treatment: 14423403 INFO @ Sun, 21 Jun 2020 18:33:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:44: #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 18:33:45: #1 tags after filtering in treatment: 14423345 INFO @ Sun, 21 Jun 2020 18:33:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:46: #2 number of paired peaks: 2577 INFO @ Sun, 21 Jun 2020 18:33:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:46: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:33:46: #2 alternative fragment length(s) may be 2,52 bps INFO @ Sun, 21 Jun 2020 18:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.20_model.r WARNING @ Sun, 21 Jun 2020 18:33:46: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:46: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Sun, 21 Jun 2020 18:33:46: #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 18:33:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.10_summits.bed INFO @ Sun, 21 Jun 2020 18:34:01: Done! pass1 - making usageList (739 chroms): 1 millis pass2 - checking and writing primary data (3287 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:34:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2417578/SRX2417578.20_summits.bed INFO @ Sun, 21 Jun 2020 18:34:26: Done! pass1 - making usageList (577 chroms): 1 millis pass2 - checking and writing primary data (1821 records, 4 fields): 17 millis CompletedMACS2peakCalling