Job ID = 12265463 SRX = SRX7192194 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9865965 spots for SRR10503239/SRR10503239.sra Written 9865965 spots for SRR10503239/SRR10503239.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265669 ("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: 00:25:17 9865965 reads; of these: 9865965 (100.00%) were paired; of these: 3231940 (32.76%) aligned concordantly 0 times 5390324 (54.64%) aligned concordantly exactly 1 time 1243701 (12.61%) aligned concordantly >1 times ---- 3231940 pairs aligned concordantly 0 times; of these: 764607 (23.66%) aligned discordantly 1 time ---- 2467333 pairs aligned 0 times concordantly or discordantly; of these: 4934666 mates make up the pairs; of these: 3500176 (70.93%) aligned 0 times 1019609 (20.66%) aligned exactly 1 time 414881 (8.41%) aligned >1 times 82.26% overall alignment rate Time searching: 00:25:17 Overall time: 00:25:17 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 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 762315 / 7222020 = 0.1056 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:44:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.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, 03 Apr 2021 07:44:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:44:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:44:59: 1000000 INFO @ Sat, 03 Apr 2021 07:45:09: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:45:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.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, 03 Apr 2021 07:45:19: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:45:19: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:45:19: 3000000 INFO @ Sat, 03 Apr 2021 07:45:28: 1000000 INFO @ Sat, 03 Apr 2021 07:45:29: 4000000 INFO @ Sat, 03 Apr 2021 07:45:37: 2000000 INFO @ Sat, 03 Apr 2021 07:45:39: 5000000 INFO @ Sat, 03 Apr 2021 07:45:46: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:45:48: 6000000 INFO @ Sat, 03 Apr 2021 07:45:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.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, 03 Apr 2021 07:45:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:45:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:45:55: 4000000 INFO @ Sat, 03 Apr 2021 07:45:58: 7000000 INFO @ Sat, 03 Apr 2021 07:45:58: 1000000 INFO @ Sat, 03 Apr 2021 07:46:03: 5000000 INFO @ Sat, 03 Apr 2021 07:46:06: 2000000 INFO @ Sat, 03 Apr 2021 07:46:07: 8000000 INFO @ Sat, 03 Apr 2021 07:46:11: 6000000 INFO @ Sat, 03 Apr 2021 07:46:15: 3000000 INFO @ Sat, 03 Apr 2021 07:46:16: 9000000 INFO @ Sat, 03 Apr 2021 07:46:20: 7000000 INFO @ Sat, 03 Apr 2021 07:46:23: 4000000 INFO @ Sat, 03 Apr 2021 07:46:25: 10000000 INFO @ Sat, 03 Apr 2021 07:46:29: 8000000 INFO @ Sat, 03 Apr 2021 07:46:32: 5000000 INFO @ Sat, 03 Apr 2021 07:46:35: 11000000 INFO @ Sat, 03 Apr 2021 07:46:37: 9000000 INFO @ Sat, 03 Apr 2021 07:46:40: 6000000 INFO @ Sat, 03 Apr 2021 07:46:44: 12000000 INFO @ Sat, 03 Apr 2021 07:46:46: 10000000 INFO @ Sat, 03 Apr 2021 07:46:49: 7000000 INFO @ Sat, 03 Apr 2021 07:46:53: 13000000 INFO @ Sat, 03 Apr 2021 07:46:54: 11000000 INFO @ Sat, 03 Apr 2021 07:46:58: 8000000 INFO @ Sat, 03 Apr 2021 07:47:03: 14000000 INFO @ Sat, 03 Apr 2021 07:47:03: 12000000 INFO @ Sat, 03 Apr 2021 07:47:07: 9000000 INFO @ Sat, 03 Apr 2021 07:47:09: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:47:09: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:47:09: #1 total tags in treatment: 5899477 INFO @ Sat, 03 Apr 2021 07:47:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:47:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:47:10: #1 tags after filtering in treatment: 5045586 INFO @ Sat, 03 Apr 2021 07:47:10: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 07:47:10: #1 finished! INFO @ Sat, 03 Apr 2021 07:47:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:47:10: #2 number of paired peaks: 1357 INFO @ Sat, 03 Apr 2021 07:47:10: start model_add_line... INFO @ Sat, 03 Apr 2021 07:47:10: start X-correlation... INFO @ Sat, 03 Apr 2021 07:47:10: end of X-cor INFO @ Sat, 03 Apr 2021 07:47:10: #2 finished! INFO @ Sat, 03 Apr 2021 07:47:10: #2 predicted fragment length is 180 bps INFO @ Sat, 03 Apr 2021 07:47:10: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 03 Apr 2021 07:47:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.05_model.r WARNING @ Sat, 03 Apr 2021 07:47:10: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:47:10: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Sat, 03 Apr 2021 07:47:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:47:10: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:47:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:47:12: 13000000 INFO @ Sat, 03 Apr 2021 07:47:15: 10000000 INFO @ Sat, 03 Apr 2021 07:47:21: 14000000 INFO @ Sat, 03 Apr 2021 07:47:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:47:24: 11000000 INFO @ Sat, 03 Apr 2021 07:47:26: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:47:26: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:47:26: #1 total tags in treatment: 5899477 INFO @ Sat, 03 Apr 2021 07:47:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:47:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:47:27: #1 tags after filtering in treatment: 5045586 INFO @ Sat, 03 Apr 2021 07:47:27: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 07:47:27: #1 finished! INFO @ Sat, 03 Apr 2021 07:47:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:47:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:47:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:47:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:47:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.05_summits.bed INFO @ Sat, 03 Apr 2021 07:47:27: Done! INFO @ Sat, 03 Apr 2021 07:47:27: #2 number of paired peaks: 1357 INFO @ Sat, 03 Apr 2021 07:47:27: start model_add_line... INFO @ Sat, 03 Apr 2021 07:47:27: start X-correlation... INFO @ Sat, 03 Apr 2021 07:47:27: end of X-cor INFO @ Sat, 03 Apr 2021 07:47:27: #2 finished! INFO @ Sat, 03 Apr 2021 07:47:27: #2 predicted fragment length is 180 bps INFO @ Sat, 03 Apr 2021 07:47:27: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 03 Apr 2021 07:47:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.10_model.r WARNING @ Sat, 03 Apr 2021 07:47:27: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:47:27: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Sat, 03 Apr 2021 07:47:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:47:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:47:27: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5997 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:47:32: 12000000 INFO @ Sat, 03 Apr 2021 07:47:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:47:39: 13000000 INFO @ Sat, 03 Apr 2021 07:47:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:47:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:47:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.10_summits.bed INFO @ Sat, 03 Apr 2021 07:47:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2935 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:47:47: 14000000 INFO @ Sat, 03 Apr 2021 07:47:52: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:47:52: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:47:52: #1 total tags in treatment: 5899477 INFO @ Sat, 03 Apr 2021 07:47:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:47:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:47:52: #1 tags after filtering in treatment: 5045586 INFO @ Sat, 03 Apr 2021 07:47:52: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 07:47:52: #1 finished! INFO @ Sat, 03 Apr 2021 07:47:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:47:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:47:52: #2 number of paired peaks: 1357 INFO @ Sat, 03 Apr 2021 07:47:52: start model_add_line... INFO @ Sat, 03 Apr 2021 07:47:52: start X-correlation... INFO @ Sat, 03 Apr 2021 07:47:52: end of X-cor INFO @ Sat, 03 Apr 2021 07:47:52: #2 finished! INFO @ Sat, 03 Apr 2021 07:47:52: #2 predicted fragment length is 180 bps INFO @ Sat, 03 Apr 2021 07:47:52: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 03 Apr 2021 07:47:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.20_model.r WARNING @ Sat, 03 Apr 2021 07:47:52: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:47:52: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Sat, 03 Apr 2021 07:47:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:47:52: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:47:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:48:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192194/SRX7192194.20_summits.bed INFO @ Sat, 03 Apr 2021 07:48:09: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (791 records, 4 fields): 3 millis CompletedMACS2peakCalling