Job ID = 6457515 SRX = SRX4664666 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:39:55 prefetch.2.10.7: 1) Downloading 'SRR7813093'... 2020-06-21T11:39:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:42:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:42:47 prefetch.2.10.7: 1) 'SRR7813093' was downloaded successfully Read 32358551 spots for SRR7813093/SRR7813093.sra Written 32358551 spots for SRR7813093/SRR7813093.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: 00:10:40 32358551 reads; of these: 32358551 (100.00%) were unpaired; of these: 1248939 (3.86%) aligned 0 times 21271564 (65.74%) aligned exactly 1 time 9838048 (30.40%) aligned >1 times 96.14% overall alignment rate Time searching: 00:10:40 Overall time: 00:10:40 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] 6715331 / 31109612 = 0.2159 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 21:02:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.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 21:02:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:02:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:02:55: 1000000 INFO @ Sun, 21 Jun 2020 21:03:03: 2000000 INFO @ Sun, 21 Jun 2020 21:03:12: 3000000 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 21:03:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.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 21:03:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:03:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:03:21: 4000000 INFO @ Sun, 21 Jun 2020 21:03:25: 1000000 INFO @ Sun, 21 Jun 2020 21:03:30: 5000000 INFO @ Sun, 21 Jun 2020 21:03:34: 2000000 INFO @ Sun, 21 Jun 2020 21:03:39: 6000000 INFO @ Sun, 21 Jun 2020 21:03:43: 3000000 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 21:03:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.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 21:03:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:03:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:03:48: 7000000 INFO @ Sun, 21 Jun 2020 21:03:53: 4000000 INFO @ Sun, 21 Jun 2020 21:03:57: 1000000 INFO @ Sun, 21 Jun 2020 21:03:57: 8000000 INFO @ Sun, 21 Jun 2020 21:04:03: 5000000 INFO @ Sun, 21 Jun 2020 21:04:06: 2000000 INFO @ Sun, 21 Jun 2020 21:04:07: 9000000 INFO @ Sun, 21 Jun 2020 21:04:12: 6000000 INFO @ Sun, 21 Jun 2020 21:04:15: 3000000 INFO @ Sun, 21 Jun 2020 21:04:16: 10000000 INFO @ Sun, 21 Jun 2020 21:04:22: 7000000 INFO @ Sun, 21 Jun 2020 21:04:24: 4000000 INFO @ Sun, 21 Jun 2020 21:04:25: 11000000 INFO @ Sun, 21 Jun 2020 21:04:32: 8000000 INFO @ Sun, 21 Jun 2020 21:04:34: 5000000 INFO @ Sun, 21 Jun 2020 21:04:34: 12000000 INFO @ Sun, 21 Jun 2020 21:04:42: 9000000 INFO @ Sun, 21 Jun 2020 21:04:43: 6000000 INFO @ Sun, 21 Jun 2020 21:04:43: 13000000 INFO @ Sun, 21 Jun 2020 21:04:51: 7000000 INFO @ Sun, 21 Jun 2020 21:04:51: 10000000 INFO @ Sun, 21 Jun 2020 21:04:52: 14000000 INFO @ Sun, 21 Jun 2020 21:05:00: 8000000 INFO @ Sun, 21 Jun 2020 21:05:00: 15000000 INFO @ Sun, 21 Jun 2020 21:05:01: 11000000 INFO @ Sun, 21 Jun 2020 21:05:09: 9000000 INFO @ Sun, 21 Jun 2020 21:05:09: 16000000 INFO @ Sun, 21 Jun 2020 21:05:11: 12000000 INFO @ Sun, 21 Jun 2020 21:05:17: 10000000 INFO @ Sun, 21 Jun 2020 21:05:18: 17000000 INFO @ Sun, 21 Jun 2020 21:05:20: 13000000 INFO @ Sun, 21 Jun 2020 21:05:26: 11000000 INFO @ Sun, 21 Jun 2020 21:05:26: 18000000 INFO @ Sun, 21 Jun 2020 21:05:29: 14000000 INFO @ Sun, 21 Jun 2020 21:05:35: 12000000 INFO @ Sun, 21 Jun 2020 21:05:35: 19000000 INFO @ Sun, 21 Jun 2020 21:05:38: 15000000 INFO @ Sun, 21 Jun 2020 21:05:43: 13000000 INFO @ Sun, 21 Jun 2020 21:05:44: 20000000 INFO @ Sun, 21 Jun 2020 21:05:46: 16000000 INFO @ Sun, 21 Jun 2020 21:05:52: 14000000 INFO @ Sun, 21 Jun 2020 21:05:53: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:05:55: 17000000 INFO @ Sun, 21 Jun 2020 21:06:01: 15000000 INFO @ Sun, 21 Jun 2020 21:06:02: 22000000 INFO @ Sun, 21 Jun 2020 21:06:04: 18000000 INFO @ Sun, 21 Jun 2020 21:06:09: 16000000 INFO @ Sun, 21 Jun 2020 21:06:11: 23000000 INFO @ Sun, 21 Jun 2020 21:06:13: 19000000 INFO @ Sun, 21 Jun 2020 21:06:18: 17000000 INFO @ Sun, 21 Jun 2020 21:06:19: 24000000 INFO @ Sun, 21 Jun 2020 21:06:22: 20000000 INFO @ Sun, 21 Jun 2020 21:06:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:06:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:06:23: #1 total tags in treatment: 24394281 INFO @ Sun, 21 Jun 2020 21:06:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:06:23: #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 21:06:24: #1 tags after filtering in treatment: 24394215 INFO @ Sun, 21 Jun 2020 21:06:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:06:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:06:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:06:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:06:25: #2 number of paired peaks: 1222 INFO @ Sun, 21 Jun 2020 21:06:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:06:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:06:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:06:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:06:26: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 21:06:26: #2 alternative fragment length(s) may be 1,60 bps INFO @ Sun, 21 Jun 2020 21:06:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.05_model.r WARNING @ Sun, 21 Jun 2020 21:06:26: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:06:26: #2 You may need to consider one of the other alternative d(s): 1,60 WARNING @ Sun, 21 Jun 2020 21:06:26: #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 21:06:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:06:26: 18000000 INFO @ Sun, 21 Jun 2020 21:06:32: 21000000 INFO @ Sun, 21 Jun 2020 21:06:34: 19000000 INFO @ Sun, 21 Jun 2020 21:06:40: 22000000 INFO @ Sun, 21 Jun 2020 21:06:42: 20000000 INFO @ Sun, 21 Jun 2020 21:06:49: 23000000 INFO @ Sun, 21 Jun 2020 21:06:50: 21000000 INFO @ Sun, 21 Jun 2020 21:06:58: 24000000 INFO @ Sun, 21 Jun 2020 21:06:58: 22000000 INFO @ Sun, 21 Jun 2020 21:07:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:07:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:07:01: #1 total tags in treatment: 24394281 INFO @ Sun, 21 Jun 2020 21:07:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:07:01: #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 21:07:02: #1 tags after filtering in treatment: 24394215 INFO @ Sun, 21 Jun 2020 21:07:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:07:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:07:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:07:04: #2 number of paired peaks: 1222 INFO @ Sun, 21 Jun 2020 21:07:04: start model_add_line... INFO @ Sun, 21 Jun 2020 21:07:04: start X-correlation... INFO @ Sun, 21 Jun 2020 21:07:04: end of X-cor INFO @ Sun, 21 Jun 2020 21:07:04: #2 finished! INFO @ Sun, 21 Jun 2020 21:07:04: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 21:07:04: #2 alternative fragment length(s) may be 1,60 bps INFO @ Sun, 21 Jun 2020 21:07:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.10_model.r WARNING @ Sun, 21 Jun 2020 21:07:04: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:07:04: #2 You may need to consider one of the other alternative d(s): 1,60 WARNING @ Sun, 21 Jun 2020 21:07:04: #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 21:07:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:07:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:07:06: 23000000 INFO @ Sun, 21 Jun 2020 21:07:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:07:14: 24000000 INFO @ Sun, 21 Jun 2020 21:07:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:07:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:07:17: #1 total tags in treatment: 24394281 INFO @ Sun, 21 Jun 2020 21:07:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:07:17: #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 21:07:18: #1 tags after filtering in treatment: 24394215 INFO @ Sun, 21 Jun 2020 21:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:07:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:07:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:07:20: #2 number of paired peaks: 1222 INFO @ Sun, 21 Jun 2020 21:07:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:07:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:07:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:07:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:07:20: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 21:07:20: #2 alternative fragment length(s) may be 1,60 bps INFO @ Sun, 21 Jun 2020 21:07:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.20_model.r WARNING @ Sun, 21 Jun 2020 21:07:20: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:07:20: #2 You may need to consider one of the other alternative d(s): 1,60 WARNING @ Sun, 21 Jun 2020 21:07:20: #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 21:07:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:07:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:07:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:07:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:07:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.05_summits.bed INFO @ Sun, 21 Jun 2020 21:07:30: Done! pass1 - making usageList (640 chroms): 2 millis pass2 - checking and writing primary data (5496 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:07:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:08:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.10_summits.bed INFO @ Sun, 21 Jun 2020 21:08:08: Done! pass1 - making usageList (562 chroms): 2 millis pass2 - checking and writing primary data (3482 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664666/SRX4664666.20_summits.bed INFO @ Sun, 21 Jun 2020 21:08:24: Done! pass1 - making usageList (464 chroms): 2 millis pass2 - checking and writing primary data (2144 records, 4 fields): 28 millis CompletedMACS2peakCalling