Job ID = 14168369 SRX = SRX8556401 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21029312 spots for SRR12024957/SRR12024957.sra Written 21029312 spots for SRR12024957/SRR12024957.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169794 ("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: 01:28:35 21029312 reads; of these: 21029312 (100.00%) were paired; of these: 11684062 (55.56%) aligned concordantly 0 times 4617029 (21.96%) aligned concordantly exactly 1 time 4728221 (22.48%) aligned concordantly >1 times ---- 11684062 pairs aligned concordantly 0 times; of these: 823513 (7.05%) aligned discordantly 1 time ---- 10860549 pairs aligned 0 times concordantly or discordantly; of these: 21721098 mates make up the pairs; of these: 15948829 (73.43%) aligned 0 times 2874389 (13.23%) aligned exactly 1 time 2897880 (13.34%) aligned >1 times 62.08% overall alignment rate Time searching: 01:28:35 Overall time: 01:28:35 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 20 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] 3689564 / 9820918 = 0.3757 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 19:55:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.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 19:55:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:55:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:55:31: 1000000 INFO @ Fri, 10 Dec 2021 19:55:42: 2000000 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 19:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.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 19:55:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:55:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:55:56: 3000000 INFO @ Fri, 10 Dec 2021 19:56:01: 1000000 INFO @ Fri, 10 Dec 2021 19:56:10: 4000000 INFO @ Fri, 10 Dec 2021 19:56:13: 2000000 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 19:56:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.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 19:56:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:56:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:56:24: 5000000 INFO @ Fri, 10 Dec 2021 19:56:25: 3000000 INFO @ Fri, 10 Dec 2021 19:56:31: 1000000 INFO @ Fri, 10 Dec 2021 19:56:38: 6000000 INFO @ Fri, 10 Dec 2021 19:56:38: 4000000 INFO @ Fri, 10 Dec 2021 19:56:43: 2000000 INFO @ Fri, 10 Dec 2021 19:56:50: 5000000 INFO @ Fri, 10 Dec 2021 19:56:51: 7000000 INFO @ Fri, 10 Dec 2021 19:56:56: 3000000 INFO @ Fri, 10 Dec 2021 19:57:02: 6000000 INFO @ Fri, 10 Dec 2021 19:57:05: 8000000 INFO @ Fri, 10 Dec 2021 19:57:08: 4000000 INFO @ Fri, 10 Dec 2021 19:57:15: 7000000 INFO @ Fri, 10 Dec 2021 19:57:18: 9000000 INFO @ Fri, 10 Dec 2021 19:57:20: 5000000 INFO @ Fri, 10 Dec 2021 19:57:27: 8000000 INFO @ Fri, 10 Dec 2021 19:57:32: 10000000 INFO @ Fri, 10 Dec 2021 19:57:32: 6000000 INFO @ Fri, 10 Dec 2021 19:57:39: 9000000 INFO @ Fri, 10 Dec 2021 19:57:45: 7000000 INFO @ Fri, 10 Dec 2021 19:57:45: 11000000 INFO @ Fri, 10 Dec 2021 19:57:52: 10000000 INFO @ Fri, 10 Dec 2021 19:57:57: 8000000 INFO @ Fri, 10 Dec 2021 19:57:59: 12000000 INFO @ Fri, 10 Dec 2021 19:58:04: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:58:09: 9000000 INFO @ Fri, 10 Dec 2021 19:58:12: 13000000 INFO @ Fri, 10 Dec 2021 19:58:17: 12000000 INFO @ Fri, 10 Dec 2021 19:58:22: 10000000 INFO @ Fri, 10 Dec 2021 19:58:25: 14000000 INFO @ Fri, 10 Dec 2021 19:58:29: 13000000 INFO @ Fri, 10 Dec 2021 19:58:34: 11000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:58:38: 15000000 INFO @ Fri, 10 Dec 2021 19:58:42: 14000000 INFO @ Fri, 10 Dec 2021 19:58:47: 12000000 INFO @ Fri, 10 Dec 2021 19:58:52: 16000000 INFO @ Fri, 10 Dec 2021 19:58:54: 15000000 INFO @ Fri, 10 Dec 2021 19:58:59: 13000000 INFO @ Fri, 10 Dec 2021 19:59:05: 17000000 INFO @ Fri, 10 Dec 2021 19:59:07: 16000000 INFO @ Fri, 10 Dec 2021 19:59:12: 14000000 INFO @ Fri, 10 Dec 2021 19:59:18: 18000000 INFO @ Fri, 10 Dec 2021 19:59:19: 17000000 INFO @ Fri, 10 Dec 2021 19:59:24: 15000000 INFO @ Fri, 10 Dec 2021 19:59:27: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 19:59:27: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 19:59:27: #1 total tags in treatment: 5771782 INFO @ Fri, 10 Dec 2021 19:59:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:59:27: #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 19:59:27: #1 tags after filtering in treatment: 4729267 INFO @ Fri, 10 Dec 2021 19:59:27: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 10 Dec 2021 19:59:27: #1 finished! INFO @ Fri, 10 Dec 2021 19:59:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:59:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:59:28: #2 number of paired peaks: 3075 INFO @ Fri, 10 Dec 2021 19:59:28: start model_add_line... INFO @ Fri, 10 Dec 2021 19:59:28: start X-correlation... INFO @ Fri, 10 Dec 2021 19:59:28: end of X-cor INFO @ Fri, 10 Dec 2021 19:59:28: #2 finished! INFO @ Fri, 10 Dec 2021 19:59:28: #2 predicted fragment length is 197 bps INFO @ Fri, 10 Dec 2021 19:59:28: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 10 Dec 2021 19:59:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.05_model.r WARNING @ Fri, 10 Dec 2021 19:59:28: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:59:28: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Fri, 10 Dec 2021 19:59:28: #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 19:59:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:59:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:59:31: 18000000 INFO @ Fri, 10 Dec 2021 19:59:36: 16000000 INFO @ Fri, 10 Dec 2021 19:59:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:59:39: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 19:59:39: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 19:59:39: #1 total tags in treatment: 5771782 INFO @ Fri, 10 Dec 2021 19:59:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:59:39: #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 19:59:39: #1 tags after filtering in treatment: 4729267 INFO @ Fri, 10 Dec 2021 19:59:39: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 10 Dec 2021 19:59:39: #1 finished! INFO @ Fri, 10 Dec 2021 19:59:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:59:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:59:40: #2 number of paired peaks: 3075 INFO @ Fri, 10 Dec 2021 19:59:40: start model_add_line... INFO @ Fri, 10 Dec 2021 19:59:40: start X-correlation... INFO @ Fri, 10 Dec 2021 19:59:40: end of X-cor INFO @ Fri, 10 Dec 2021 19:59:40: #2 finished! INFO @ Fri, 10 Dec 2021 19:59:40: #2 predicted fragment length is 197 bps INFO @ Fri, 10 Dec 2021 19:59:40: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 10 Dec 2021 19:59:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.10_model.r WARNING @ Fri, 10 Dec 2021 19:59:40: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:59:40: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Fri, 10 Dec 2021 19:59:40: #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 19:59:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:59:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:59:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:59:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:59:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.05_summits.bed INFO @ Fri, 10 Dec 2021 19:59:45: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12721 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:59:47: 17000000 INFO @ Fri, 10 Dec 2021 19:59:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:59:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:59:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:59:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.10_summits.bed INFO @ Fri, 10 Dec 2021 19:59:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7998 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:59:57: 18000000 INFO @ Fri, 10 Dec 2021 20:00:04: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 20:00:04: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 20:00:04: #1 total tags in treatment: 5771782 INFO @ Fri, 10 Dec 2021 20:00:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:00:04: #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 20:00:04: #1 tags after filtering in treatment: 4729267 INFO @ Fri, 10 Dec 2021 20:00:04: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 10 Dec 2021 20:00:04: #1 finished! INFO @ Fri, 10 Dec 2021 20:00:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:00:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:00:05: #2 number of paired peaks: 3075 INFO @ Fri, 10 Dec 2021 20:00:05: start model_add_line... INFO @ Fri, 10 Dec 2021 20:00:05: start X-correlation... INFO @ Fri, 10 Dec 2021 20:00:05: end of X-cor INFO @ Fri, 10 Dec 2021 20:00:05: #2 finished! INFO @ Fri, 10 Dec 2021 20:00:05: #2 predicted fragment length is 197 bps INFO @ Fri, 10 Dec 2021 20:00:05: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 10 Dec 2021 20:00:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.20_model.r WARNING @ Fri, 10 Dec 2021 20:00:05: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:00:05: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Fri, 10 Dec 2021 20:00:05: #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 20:00:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:00:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:00:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:00:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:00:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:00:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556401/SRX8556401.20_summits.bed INFO @ Fri, 10 Dec 2021 20:00:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3603 records, 4 fields): 5 millis CompletedMACS2peakCalling