Job ID = 10166191 SRX = SRX7723711 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 35759716 spots for SRR11084667/SRR11084667.sra Written 35759716 spots for SRR11084667/SRR11084667.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166657 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:32 35759716 reads; of these: 35759716 (100.00%) were unpaired; of these: 2463910 (6.89%) aligned 0 times 26526525 (74.18%) aligned exactly 1 time 6769281 (18.93%) aligned >1 times 93.11% overall alignment rate Time searching: 00:18:32 Overall time: 00:18:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 11607536 / 33295806 = 0.3486 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 @ Thu, 08 Oct 2020 21:04:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.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 @ Thu, 08 Oct 2020 21:04:50: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:04:50: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:04:57: 1000000 INFO @ Thu, 08 Oct 2020 21:05:03: 2000000 INFO @ Thu, 08 Oct 2020 21:05:10: 3000000 INFO @ Thu, 08 Oct 2020 21:05:16: 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 @ Thu, 08 Oct 2020 21:05:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.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 @ Thu, 08 Oct 2020 21:05:20: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:05:20: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:05:23: 5000000 INFO @ Thu, 08 Oct 2020 21:05:28: 1000000 INFO @ Thu, 08 Oct 2020 21:05:30: 6000000 INFO @ Thu, 08 Oct 2020 21:05:35: 2000000 INFO @ Thu, 08 Oct 2020 21:05:37: 7000000 INFO @ Thu, 08 Oct 2020 21:05:43: 3000000 INFO @ Thu, 08 Oct 2020 21:05:45: 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 @ Thu, 08 Oct 2020 21:05:50: 4000000 INFO @ Thu, 08 Oct 2020 21:05:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.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 @ Thu, 08 Oct 2020 21:05:50: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:05:50: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:05:52: 9000000 INFO @ Thu, 08 Oct 2020 21:05:58: 5000000 INFO @ Thu, 08 Oct 2020 21:06:00: 10000000 INFO @ Thu, 08 Oct 2020 21:06:00: 1000000 INFO @ Thu, 08 Oct 2020 21:06:06: 6000000 INFO @ Thu, 08 Oct 2020 21:06:09: 11000000 INFO @ Thu, 08 Oct 2020 21:06:14: 2000000 INFO @ Thu, 08 Oct 2020 21:06:14: 7000000 INFO @ Thu, 08 Oct 2020 21:06:17: 12000000 INFO @ Thu, 08 Oct 2020 21:06:23: 8000000 INFO @ Thu, 08 Oct 2020 21:06:25: 13000000 INFO @ Thu, 08 Oct 2020 21:06:27: 3000000 INFO @ Thu, 08 Oct 2020 21:06:31: 9000000 INFO @ Thu, 08 Oct 2020 21:06:33: 14000000 INFO @ Thu, 08 Oct 2020 21:06:39: 10000000 INFO @ Thu, 08 Oct 2020 21:06:40: 4000000 INFO @ Thu, 08 Oct 2020 21:06:41: 15000000 INFO @ Thu, 08 Oct 2020 21:06:48: 11000000 INFO @ Thu, 08 Oct 2020 21:06:50: 16000000 INFO @ Thu, 08 Oct 2020 21:06:53: 5000000 INFO @ Thu, 08 Oct 2020 21:06:56: 12000000 INFO @ Thu, 08 Oct 2020 21:06:58: 17000000 INFO @ Thu, 08 Oct 2020 21:07:04: 13000000 INFO @ Thu, 08 Oct 2020 21:07:06: 6000000 INFO @ Thu, 08 Oct 2020 21:07:06: 18000000 INFO @ Thu, 08 Oct 2020 21:07:12: 14000000 INFO @ Thu, 08 Oct 2020 21:07:15: 19000000 INFO @ Thu, 08 Oct 2020 21:07:19: 7000000 INFO @ Thu, 08 Oct 2020 21:07:21: 15000000 INFO @ Thu, 08 Oct 2020 21:07:23: 20000000 INFO @ Thu, 08 Oct 2020 21:07:29: 16000000 INFO @ Thu, 08 Oct 2020 21:07:31: 21000000 INFO @ Thu, 08 Oct 2020 21:07:32: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 21:07:37: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:07:37: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:07:37: #1 total tags in treatment: 21688270 INFO @ Thu, 08 Oct 2020 21:07:37: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:07:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:07:37: #1 tags after filtering in treatment: 21688270 INFO @ Thu, 08 Oct 2020 21:07:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:07:37: #1 finished! INFO @ Thu, 08 Oct 2020 21:07:37: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:07:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:07:37: 17000000 INFO @ Thu, 08 Oct 2020 21:07:39: #2 number of paired peaks: 1382 INFO @ Thu, 08 Oct 2020 21:07:39: start model_add_line... INFO @ Thu, 08 Oct 2020 21:07:39: start X-correlation... INFO @ Thu, 08 Oct 2020 21:07:39: end of X-cor INFO @ Thu, 08 Oct 2020 21:07:39: #2 finished! INFO @ Thu, 08 Oct 2020 21:07:39: #2 predicted fragment length is 95 bps INFO @ Thu, 08 Oct 2020 21:07:39: #2 alternative fragment length(s) may be 95 bps INFO @ Thu, 08 Oct 2020 21:07:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.05_model.r WARNING @ Thu, 08 Oct 2020 21:07:39: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:07:39: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Thu, 08 Oct 2020 21:07:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:07:39: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:07:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:07:45: 18000000 INFO @ Thu, 08 Oct 2020 21:07:46: 9000000 INFO @ Thu, 08 Oct 2020 21:07:53: 19000000 INFO @ Thu, 08 Oct 2020 21:07:58: 10000000 INFO @ Thu, 08 Oct 2020 21:08:01: 20000000 INFO @ Thu, 08 Oct 2020 21:08:09: 21000000 INFO @ Thu, 08 Oct 2020 21:08:11: 11000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 21:08:15: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:08:15: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:08:15: #1 total tags in treatment: 21688270 INFO @ Thu, 08 Oct 2020 21:08:15: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:08:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:08:15: #1 tags after filtering in treatment: 21688270 INFO @ Thu, 08 Oct 2020 21:08:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:08:15: #1 finished! INFO @ Thu, 08 Oct 2020 21:08:15: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:08:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:08:17: #2 number of paired peaks: 1382 INFO @ Thu, 08 Oct 2020 21:08:17: start model_add_line... INFO @ Thu, 08 Oct 2020 21:08:17: start X-correlation... INFO @ Thu, 08 Oct 2020 21:08:17: end of X-cor INFO @ Thu, 08 Oct 2020 21:08:17: #2 finished! INFO @ Thu, 08 Oct 2020 21:08:17: #2 predicted fragment length is 95 bps INFO @ Thu, 08 Oct 2020 21:08:17: #2 alternative fragment length(s) may be 95 bps INFO @ Thu, 08 Oct 2020 21:08:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.10_model.r WARNING @ Thu, 08 Oct 2020 21:08:17: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:08:17: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Thu, 08 Oct 2020 21:08:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:08:17: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:08:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:08:23: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:08:24: 12000000 INFO @ Thu, 08 Oct 2020 21:08:37: 13000000 INFO @ Thu, 08 Oct 2020 21:08:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.05_peaks.xls INFO @ Thu, 08 Oct 2020 21:08:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:08:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.05_summits.bed INFO @ Thu, 08 Oct 2020 21:08:47: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (47836 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:08:49: 14000000 INFO @ Thu, 08 Oct 2020 21:09:00: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:09:02: 15000000 INFO @ Thu, 08 Oct 2020 21:09:13: 16000000 INFO @ Thu, 08 Oct 2020 21:09:21: 17000000 INFO @ Thu, 08 Oct 2020 21:09:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.10_peaks.xls INFO @ Thu, 08 Oct 2020 21:09:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.10_summits.bed INFO @ Thu, 08 Oct 2020 21:09:24: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (32592 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:09:29: 18000000 INFO @ Thu, 08 Oct 2020 21:09:37: 19000000 INFO @ Thu, 08 Oct 2020 21:09:46: 20000000 INFO @ Thu, 08 Oct 2020 21:09:54: 21000000 INFO @ Thu, 08 Oct 2020 21:10:00: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:10:00: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:10:00: #1 total tags in treatment: 21688270 INFO @ Thu, 08 Oct 2020 21:10:00: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:10:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:10:00: #1 tags after filtering in treatment: 21688270 INFO @ Thu, 08 Oct 2020 21:10:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:10:00: #1 finished! INFO @ Thu, 08 Oct 2020 21:10:00: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:10:02: #2 number of paired peaks: 1382 INFO @ Thu, 08 Oct 2020 21:10:02: start model_add_line... INFO @ Thu, 08 Oct 2020 21:10:02: start X-correlation... INFO @ Thu, 08 Oct 2020 21:10:02: end of X-cor INFO @ Thu, 08 Oct 2020 21:10:02: #2 finished! INFO @ Thu, 08 Oct 2020 21:10:02: #2 predicted fragment length is 95 bps INFO @ Thu, 08 Oct 2020 21:10:02: #2 alternative fragment length(s) may be 95 bps INFO @ Thu, 08 Oct 2020 21:10:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.20_model.r WARNING @ Thu, 08 Oct 2020 21:10:02: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:10:02: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Thu, 08 Oct 2020 21:10:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:10:02: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:10:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:10:45: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:11:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.20_peaks.xls INFO @ Thu, 08 Oct 2020 21:11:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:11:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723711/SRX7723711.20_summits.bed INFO @ Thu, 08 Oct 2020 21:11:08: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (16434 records, 4 fields): 16 millis CompletedMACS2peakCalling