Job ID = 14171467 SRX = SRX9137158 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5842503 spots for SRR12655988/SRR12655988.sra Written 5842503 spots for SRR12655988/SRR12655988.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171962 ("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: 00:05:51 5842503 reads; of these: 5842503 (100.00%) were unpaired; of these: 793114 (13.57%) aligned 0 times 4029063 (68.96%) aligned exactly 1 time 1020326 (17.46%) aligned >1 times 86.43% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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_rmdupse_core] 267264 / 5049389 = 0.0529 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:54:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.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 @ Sat, 11 Dec 2021 11:54:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:54:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:55:07: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:55:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.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 @ Sat, 11 Dec 2021 11:55:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:55:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:55:22: 2000000 INFO @ Sat, 11 Dec 2021 11:55:38: 3000000 INFO @ Sat, 11 Dec 2021 11:55:39: 1000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:55:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.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 @ Sat, 11 Dec 2021 11:55:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:55:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:55:53: 4000000 INFO @ Sat, 11 Dec 2021 11:55:56: 2000000 INFO @ Sat, 11 Dec 2021 11:56:05: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 11:56:05: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 11:56:05: #1 total tags in treatment: 4782125 INFO @ Sat, 11 Dec 2021 11:56:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:56:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:56:05: #1 tags after filtering in treatment: 4782125 INFO @ Sat, 11 Dec 2021 11:56:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:56:05: #1 finished! INFO @ Sat, 11 Dec 2021 11:56:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:56:06: #2 number of paired peaks: 1488 INFO @ Sat, 11 Dec 2021 11:56:06: start model_add_line... INFO @ Sat, 11 Dec 2021 11:56:06: start X-correlation... INFO @ Sat, 11 Dec 2021 11:56:06: end of X-cor INFO @ Sat, 11 Dec 2021 11:56:06: #2 finished! INFO @ Sat, 11 Dec 2021 11:56:06: #2 predicted fragment length is 163 bps INFO @ Sat, 11 Dec 2021 11:56:06: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 11 Dec 2021 11:56:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.05_model.r WARNING @ Sat, 11 Dec 2021 11:56:06: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:56:06: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Sat, 11 Dec 2021 11:56:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:56:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:56:07: 1000000 INFO @ Sat, 11 Dec 2021 11:56:12: 3000000 INFO @ Sat, 11 Dec 2021 11:56:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:56:23: 2000000 INFO @ Sat, 11 Dec 2021 11:56:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:56:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:56:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.05_summits.bed INFO @ Sat, 11 Dec 2021 11:56:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5494 records, 4 fields): 113 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:56:29: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:56:38: 3000000 INFO @ Sat, 11 Dec 2021 11:56:41: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 11:56:41: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 11:56:41: #1 total tags in treatment: 4782125 INFO @ Sat, 11 Dec 2021 11:56:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:56:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:56:42: #1 tags after filtering in treatment: 4782125 INFO @ Sat, 11 Dec 2021 11:56:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:56:42: #1 finished! INFO @ Sat, 11 Dec 2021 11:56:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:56:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:56:42: #2 number of paired peaks: 1488 INFO @ Sat, 11 Dec 2021 11:56:42: start model_add_line... INFO @ Sat, 11 Dec 2021 11:56:42: start X-correlation... INFO @ Sat, 11 Dec 2021 11:56:42: end of X-cor INFO @ Sat, 11 Dec 2021 11:56:42: #2 finished! INFO @ Sat, 11 Dec 2021 11:56:42: #2 predicted fragment length is 163 bps INFO @ Sat, 11 Dec 2021 11:56:42: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 11 Dec 2021 11:56:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.10_model.r WARNING @ Sat, 11 Dec 2021 11:56:42: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:56:42: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Sat, 11 Dec 2021 11:56:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:56:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:56:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:56:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:56:54: 4000000 INFO @ Sat, 11 Dec 2021 11:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.10_summits.bed INFO @ Sat, 11 Dec 2021 11:57:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2471 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:57:06: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 11:57:06: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 11:57:06: #1 total tags in treatment: 4782125 INFO @ Sat, 11 Dec 2021 11:57:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:57:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:57:06: #1 tags after filtering in treatment: 4782125 INFO @ Sat, 11 Dec 2021 11:57:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:57:06: #1 finished! INFO @ Sat, 11 Dec 2021 11:57:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:57:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:57:06: #2 number of paired peaks: 1488 INFO @ Sat, 11 Dec 2021 11:57:06: start model_add_line... INFO @ Sat, 11 Dec 2021 11:57:06: start X-correlation... INFO @ Sat, 11 Dec 2021 11:57:06: end of X-cor INFO @ Sat, 11 Dec 2021 11:57:06: #2 finished! INFO @ Sat, 11 Dec 2021 11:57:06: #2 predicted fragment length is 163 bps INFO @ Sat, 11 Dec 2021 11:57:06: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 11 Dec 2021 11:57:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.20_model.r WARNING @ Sat, 11 Dec 2021 11:57:06: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:57:06: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Sat, 11 Dec 2021 11:57:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:57:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:57:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:57:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:57:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:57:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:57:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9137158/SRX9137158.20_summits.bed INFO @ Sat, 11 Dec 2021 11:57:25: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (575 records, 4 fields): 55 millis CompletedMACS2peakCalling