Job ID = 14167213 SRX = SRX8913799 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17536874 spots for SRR12417798/SRR12417798.sra Written 17536874 spots for SRR12417798/SRR12417798.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168689 ("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: 03:27:39 17536874 reads; of these: 17536874 (100.00%) were paired; of these: 5633745 (32.13%) aligned concordantly 0 times 2993483 (17.07%) aligned concordantly exactly 1 time 8909646 (50.81%) aligned concordantly >1 times ---- 5633745 pairs aligned concordantly 0 times; of these: 837588 (14.87%) aligned discordantly 1 time ---- 4796157 pairs aligned 0 times concordantly or discordantly; of these: 9592314 mates make up the pairs; of these: 6305607 (65.74%) aligned 0 times 353762 (3.69%) aligned exactly 1 time 2932945 (30.58%) aligned >1 times 82.02% overall alignment rate Time searching: 03:27:39 Overall time: 03:27:39 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 24 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] 3087990 / 12518122 = 0.2467 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 @ Fri, 10 Dec 2021 14:48:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.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 @ Fri, 10 Dec 2021 14:48:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:48:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:48:14: 1000000 INFO @ Fri, 10 Dec 2021 14:48:20: 2000000 INFO @ Fri, 10 Dec 2021 14:48:27: 3000000 INFO @ Fri, 10 Dec 2021 14:48:33: 4000000 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 @ Fri, 10 Dec 2021 14:48:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.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 @ Fri, 10 Dec 2021 14:48:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:48:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:48:40: 5000000 INFO @ Fri, 10 Dec 2021 14:48:44: 1000000 INFO @ Fri, 10 Dec 2021 14:48:47: 6000000 INFO @ Fri, 10 Dec 2021 14:48:51: 2000000 INFO @ Fri, 10 Dec 2021 14:48:54: 7000000 INFO @ Fri, 10 Dec 2021 14:48:58: 3000000 INFO @ Fri, 10 Dec 2021 14:49:00: 8000000 INFO @ Fri, 10 Dec 2021 14:49:05: 4000000 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 @ Fri, 10 Dec 2021 14:49:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.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 @ Fri, 10 Dec 2021 14:49:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:49:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:49:07: 9000000 INFO @ Fri, 10 Dec 2021 14:49:12: 5000000 INFO @ Fri, 10 Dec 2021 14:49:14: 1000000 INFO @ Fri, 10 Dec 2021 14:49:14: 10000000 INFO @ Fri, 10 Dec 2021 14:49:19: 6000000 INFO @ Fri, 10 Dec 2021 14:49:21: 11000000 INFO @ Fri, 10 Dec 2021 14:49:22: 2000000 INFO @ Fri, 10 Dec 2021 14:49:26: 7000000 INFO @ Fri, 10 Dec 2021 14:49:28: 12000000 INFO @ Fri, 10 Dec 2021 14:49:29: 3000000 INFO @ Fri, 10 Dec 2021 14:49:33: 8000000 INFO @ Fri, 10 Dec 2021 14:49:35: 13000000 INFO @ Fri, 10 Dec 2021 14:49:36: 4000000 INFO @ Fri, 10 Dec 2021 14:49:40: 9000000 INFO @ Fri, 10 Dec 2021 14:49:42: 14000000 INFO @ Fri, 10 Dec 2021 14:49:44: 5000000 INFO @ Fri, 10 Dec 2021 14:49:47: 10000000 INFO @ Fri, 10 Dec 2021 14:49:49: 15000000 INFO @ Fri, 10 Dec 2021 14:49:51: 6000000 INFO @ Fri, 10 Dec 2021 14:49:54: 11000000 INFO @ Fri, 10 Dec 2021 14:49:56: 16000000 INFO @ Fri, 10 Dec 2021 14:49:59: 7000000 INFO @ Fri, 10 Dec 2021 14:50:01: 12000000 INFO @ Fri, 10 Dec 2021 14:50:03: 17000000 INFO @ Fri, 10 Dec 2021 14:50:06: 8000000 INFO @ Fri, 10 Dec 2021 14:50:08: 13000000 INFO @ Fri, 10 Dec 2021 14:50:11: 18000000 INFO @ Fri, 10 Dec 2021 14:50:13: 9000000 INFO @ Fri, 10 Dec 2021 14:50:15: 14000000 INFO @ Fri, 10 Dec 2021 14:50:18: 19000000 INFO @ Fri, 10 Dec 2021 14:50:20: 10000000 INFO @ Fri, 10 Dec 2021 14:50:22: 15000000 INFO @ Fri, 10 Dec 2021 14:50:25: 20000000 INFO @ Fri, 10 Dec 2021 14:50:27: 11000000 INFO @ Fri, 10 Dec 2021 14:50:29: 16000000 INFO @ Fri, 10 Dec 2021 14:50:33: 21000000 INFO @ Fri, 10 Dec 2021 14:50:34: 12000000 INFO @ Fri, 10 Dec 2021 14:50:37: 17000000 INFO @ Fri, 10 Dec 2021 14:50:40: 22000000 INFO @ Fri, 10 Dec 2021 14:50:42: 13000000 INFO @ Fri, 10 Dec 2021 14:50:44: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 14:50:44: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 14:50:44: #1 total tags in treatment: 8886133 INFO @ Fri, 10 Dec 2021 14:50:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:50:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:50:44: #1 tags after filtering in treatment: 6383594 INFO @ Fri, 10 Dec 2021 14:50:44: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 14:50:44: #1 finished! INFO @ Fri, 10 Dec 2021 14:50:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:50:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:50:44: 18000000 INFO @ Fri, 10 Dec 2021 14:50:45: #2 number of paired peaks: 2854 INFO @ Fri, 10 Dec 2021 14:50:45: start model_add_line... INFO @ Fri, 10 Dec 2021 14:50:45: start X-correlation... INFO @ Fri, 10 Dec 2021 14:50:45: end of X-cor INFO @ Fri, 10 Dec 2021 14:50:45: #2 finished! INFO @ Fri, 10 Dec 2021 14:50:45: #2 predicted fragment length is 188 bps INFO @ Fri, 10 Dec 2021 14:50:45: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 10 Dec 2021 14:50:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.05_model.r WARNING @ Fri, 10 Dec 2021 14:50:45: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:50:45: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Fri, 10 Dec 2021 14:50:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:50:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:50:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:50:49: 14000000 INFO @ Fri, 10 Dec 2021 14:50:52: 19000000 INFO @ Fri, 10 Dec 2021 14:50:55: 15000000 INFO @ Fri, 10 Dec 2021 14:50:59: 20000000 INFO @ Fri, 10 Dec 2021 14:51:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:51:03: 16000000 INFO @ Fri, 10 Dec 2021 14:51:07: 21000000 INFO @ Fri, 10 Dec 2021 14:51:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:51:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:51:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.05_summits.bed INFO @ Fri, 10 Dec 2021 14:51:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8997 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:51:10: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:51:14: 22000000 INFO @ Fri, 10 Dec 2021 14:51:17: 18000000 INFO @ Fri, 10 Dec 2021 14:51:18: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 14:51:18: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 14:51:18: #1 total tags in treatment: 8886133 INFO @ Fri, 10 Dec 2021 14:51:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:51:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:51:19: #1 tags after filtering in treatment: 6383594 INFO @ Fri, 10 Dec 2021 14:51:19: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 14:51:19: #1 finished! INFO @ Fri, 10 Dec 2021 14:51:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:51:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:51:19: #2 number of paired peaks: 2854 INFO @ Fri, 10 Dec 2021 14:51:19: start model_add_line... INFO @ Fri, 10 Dec 2021 14:51:19: start X-correlation... INFO @ Fri, 10 Dec 2021 14:51:19: end of X-cor INFO @ Fri, 10 Dec 2021 14:51:19: #2 finished! INFO @ Fri, 10 Dec 2021 14:51:19: #2 predicted fragment length is 188 bps INFO @ Fri, 10 Dec 2021 14:51:19: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 10 Dec 2021 14:51:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.10_model.r WARNING @ Fri, 10 Dec 2021 14:51:19: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:51:19: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Fri, 10 Dec 2021 14:51:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:51:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:51:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:51:25: 19000000 INFO @ Fri, 10 Dec 2021 14:51:32: 20000000 INFO @ Fri, 10 Dec 2021 14:51:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:51:39: 21000000 INFO @ Fri, 10 Dec 2021 14:51:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:51:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:51:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.10_summits.bed INFO @ Fri, 10 Dec 2021 14:51:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5401 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 14:51:46: 22000000 INFO @ Fri, 10 Dec 2021 14:51:50: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 14:51:50: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 14:51:50: #1 total tags in treatment: 8886133 INFO @ Fri, 10 Dec 2021 14:51:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:51:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:51:50: #1 tags after filtering in treatment: 6383594 INFO @ Fri, 10 Dec 2021 14:51:50: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 14:51:50: #1 finished! INFO @ Fri, 10 Dec 2021 14:51:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:51:51: #2 number of paired peaks: 2854 INFO @ Fri, 10 Dec 2021 14:51:51: start model_add_line... INFO @ Fri, 10 Dec 2021 14:51:51: start X-correlation... INFO @ Fri, 10 Dec 2021 14:51:51: end of X-cor INFO @ Fri, 10 Dec 2021 14:51:51: #2 finished! INFO @ Fri, 10 Dec 2021 14:51:51: #2 predicted fragment length is 188 bps INFO @ Fri, 10 Dec 2021 14:51:51: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 10 Dec 2021 14:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.20_model.r WARNING @ Fri, 10 Dec 2021 14:51:51: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:51:51: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Fri, 10 Dec 2021 14:51:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:51:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:52:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:52:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:52:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:52:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913799/SRX8913799.20_summits.bed INFO @ Fri, 10 Dec 2021 14:52:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2783 records, 4 fields): 134 millis CompletedMACS2peakCalling