Job ID = 12265327 SRX = SRX5736455 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16748363 spots for SRR8956866/SRR8956866.sra Written 16748363 spots for SRR8956866/SRR8956866.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265514 ("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: 00:14:00 16748363 reads; of these: 16748363 (100.00%) were paired; of these: 8145275 (48.63%) aligned concordantly 0 times 1456643 (8.70%) aligned concordantly exactly 1 time 7146445 (42.67%) aligned concordantly >1 times ---- 8145275 pairs aligned concordantly 0 times; of these: 135484 (1.66%) aligned discordantly 1 time ---- 8009791 pairs aligned 0 times concordantly or discordantly; of these: 16019582 mates make up the pairs; of these: 14809906 (92.45%) aligned 0 times 91557 (0.57%) aligned exactly 1 time 1118119 (6.98%) aligned >1 times 55.79% overall alignment rate Time searching: 00:14:00 Overall time: 00:14:00 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] 5532922 / 8681693 = 0.6373 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 06:56:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.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 06:56:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:56:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:56:40: 1000000 INFO @ Sat, 03 Apr 2021 06:56:46: 2000000 INFO @ Sat, 03 Apr 2021 06:56:52: 3000000 INFO @ Sat, 03 Apr 2021 06:56:57: 4000000 INFO @ Sat, 03 Apr 2021 06:57:02: 5000000 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 06:57:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.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 06:57:04: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:57:04: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:57:08: 6000000 INFO @ Sat, 03 Apr 2021 06:57:11: 1000000 INFO @ Sat, 03 Apr 2021 06:57:14: 7000000 INFO @ Sat, 03 Apr 2021 06:57:17: 2000000 INFO @ Sat, 03 Apr 2021 06:57:18: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:57:18: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:57:18: #1 total tags in treatment: 3086995 INFO @ Sat, 03 Apr 2021 06:57:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:57:18: #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 06:57:18: #1 tags after filtering in treatment: 1789973 INFO @ Sat, 03 Apr 2021 06:57:18: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 03 Apr 2021 06:57:18: #1 finished! INFO @ Sat, 03 Apr 2021 06:57:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:57:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:57:18: #2 number of paired peaks: 1039 INFO @ Sat, 03 Apr 2021 06:57:18: start model_add_line... INFO @ Sat, 03 Apr 2021 06:57:19: start X-correlation... INFO @ Sat, 03 Apr 2021 06:57:19: end of X-cor INFO @ Sat, 03 Apr 2021 06:57:19: #2 finished! INFO @ Sat, 03 Apr 2021 06:57:19: #2 predicted fragment length is 125 bps INFO @ Sat, 03 Apr 2021 06:57:19: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 03 Apr 2021 06:57:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.05_model.r WARNING @ Sat, 03 Apr 2021 06:57:19: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:57:19: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Sat, 03 Apr 2021 06:57:19: #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 06:57:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:57:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:57:23: 3000000 INFO @ Sat, 03 Apr 2021 06:57:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:57:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:57:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:57:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.05_summits.bed INFO @ Sat, 03 Apr 2021 06:57:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1175 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:57:28: 4000000 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 06:57:34: 5000000 INFO @ Sat, 03 Apr 2021 06:57:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.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 06:57:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:57:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:57:40: 6000000 INFO @ Sat, 03 Apr 2021 06:57:41: 1000000 INFO @ Sat, 03 Apr 2021 06:57:46: 7000000 INFO @ Sat, 03 Apr 2021 06:57:47: 2000000 INFO @ Sat, 03 Apr 2021 06:57:50: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:57:50: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:57:50: #1 total tags in treatment: 3086995 INFO @ Sat, 03 Apr 2021 06:57:50: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:57:50: #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 06:57:50: #1 tags after filtering in treatment: 1789973 INFO @ Sat, 03 Apr 2021 06:57:50: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 03 Apr 2021 06:57:50: #1 finished! INFO @ Sat, 03 Apr 2021 06:57:50: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:57:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:57:50: #2 number of paired peaks: 1039 INFO @ Sat, 03 Apr 2021 06:57:50: start model_add_line... INFO @ Sat, 03 Apr 2021 06:57:50: start X-correlation... INFO @ Sat, 03 Apr 2021 06:57:50: end of X-cor INFO @ Sat, 03 Apr 2021 06:57:50: #2 finished! INFO @ Sat, 03 Apr 2021 06:57:50: #2 predicted fragment length is 125 bps INFO @ Sat, 03 Apr 2021 06:57:50: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 03 Apr 2021 06:57:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.10_model.r WARNING @ Sat, 03 Apr 2021 06:57:50: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:57:50: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Sat, 03 Apr 2021 06:57:50: #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 06:57:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:57:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:57:53: 3000000 INFO @ Sat, 03 Apr 2021 06:57:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:57:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:57:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:57:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.10_summits.bed INFO @ Sat, 03 Apr 2021 06:57:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (643 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:57:59: 4000000 INFO @ Sat, 03 Apr 2021 06:58:04: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:58:09: 6000000 INFO @ Sat, 03 Apr 2021 06:58:15: 7000000 INFO @ Sat, 03 Apr 2021 06:58:19: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:58:19: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:58:19: #1 total tags in treatment: 3086995 INFO @ Sat, 03 Apr 2021 06:58:19: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:58:19: #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 06:58:19: #1 tags after filtering in treatment: 1789973 INFO @ Sat, 03 Apr 2021 06:58:19: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 03 Apr 2021 06:58:19: #1 finished! INFO @ Sat, 03 Apr 2021 06:58:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:58:19: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:58:19: #2 number of paired peaks: 1039 INFO @ Sat, 03 Apr 2021 06:58:19: start model_add_line... INFO @ Sat, 03 Apr 2021 06:58:19: start X-correlation... INFO @ Sat, 03 Apr 2021 06:58:19: end of X-cor INFO @ Sat, 03 Apr 2021 06:58:19: #2 finished! INFO @ Sat, 03 Apr 2021 06:58:19: #2 predicted fragment length is 125 bps INFO @ Sat, 03 Apr 2021 06:58:19: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 03 Apr 2021 06:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.20_model.r WARNING @ Sat, 03 Apr 2021 06:58:19: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:58:19: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Sat, 03 Apr 2021 06:58:19: #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 06:58:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:58:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:58:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:58:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:58:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736455/SRX5736455.20_summits.bed INFO @ Sat, 03 Apr 2021 06:58:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (340 records, 4 fields): 2 millis CompletedMACS2peakCalling