Job ID = 14172110 SRX = SRX9103815 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23055379 spots for SRR12621015/SRR12621015.sra Written 23055379 spots for SRR12621015/SRR12621015.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172645 ("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: 00:26:20 23055379 reads; of these: 23055379 (100.00%) were paired; of these: 10461729 (45.38%) aligned concordantly 0 times 6960033 (30.19%) aligned concordantly exactly 1 time 5633617 (24.44%) aligned concordantly >1 times ---- 10461729 pairs aligned concordantly 0 times; of these: 1331140 (12.72%) aligned discordantly 1 time ---- 9130589 pairs aligned 0 times concordantly or discordantly; of these: 18261178 mates make up the pairs; of these: 16305911 (89.29%) aligned 0 times 502752 (2.75%) aligned exactly 1 time 1452515 (7.95%) aligned >1 times 64.64% overall alignment rate Time searching: 00:26:20 Overall time: 00:26:20 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 16 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] 4133975 / 13734514 = 0.3010 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 14:54:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.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 14:54:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:54:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:55:07: 1000000 INFO @ Sat, 11 Dec 2021 14:55:18: 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 @ Sat, 11 Dec 2021 14:55:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.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 14:55:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:55:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:55:28: 3000000 INFO @ Sat, 11 Dec 2021 14:55:37: 1000000 INFO @ Sat, 11 Dec 2021 14:55:38: 4000000 INFO @ Sat, 11 Dec 2021 14:55:47: 2000000 INFO @ Sat, 11 Dec 2021 14:55:48: 5000000 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 14:55:57: 3000000 INFO @ Sat, 11 Dec 2021 14:55:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.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 14:55:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:55:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:55:58: 6000000 INFO @ Sat, 11 Dec 2021 14:56:07: 4000000 INFO @ Sat, 11 Dec 2021 14:56:07: 1000000 INFO @ Sat, 11 Dec 2021 14:56:07: 7000000 INFO @ Sat, 11 Dec 2021 14:56:16: 5000000 INFO @ Sat, 11 Dec 2021 14:56:17: 2000000 INFO @ Sat, 11 Dec 2021 14:56:17: 8000000 INFO @ Sat, 11 Dec 2021 14:56:26: 6000000 INFO @ Sat, 11 Dec 2021 14:56:26: 3000000 INFO @ Sat, 11 Dec 2021 14:56:27: 9000000 INFO @ Sat, 11 Dec 2021 14:56:35: 7000000 INFO @ Sat, 11 Dec 2021 14:56:35: 4000000 INFO @ Sat, 11 Dec 2021 14:56:38: 10000000 INFO @ Sat, 11 Dec 2021 14:56:45: 8000000 INFO @ Sat, 11 Dec 2021 14:56:45: 5000000 INFO @ Sat, 11 Dec 2021 14:56:48: 11000000 INFO @ Sat, 11 Dec 2021 14:56:55: 6000000 INFO @ Sat, 11 Dec 2021 14:56:56: 9000000 INFO @ Sat, 11 Dec 2021 14:56:58: 12000000 INFO @ Sat, 11 Dec 2021 14:57:06: 7000000 INFO @ Sat, 11 Dec 2021 14:57:06: 10000000 INFO @ Sat, 11 Dec 2021 14:57:09: 13000000 INFO @ Sat, 11 Dec 2021 14:57:16: 8000000 INFO @ Sat, 11 Dec 2021 14:57:17: 11000000 INFO @ Sat, 11 Dec 2021 14:57:19: 14000000 INFO @ Sat, 11 Dec 2021 14:57:27: 9000000 INFO @ Sat, 11 Dec 2021 14:57:27: 12000000 INFO @ Sat, 11 Dec 2021 14:57:29: 15000000 INFO @ Sat, 11 Dec 2021 14:57:37: 10000000 INFO @ Sat, 11 Dec 2021 14:57:37: 13000000 INFO @ Sat, 11 Dec 2021 14:57:38: 16000000 INFO @ Sat, 11 Dec 2021 14:57:47: 11000000 INFO @ Sat, 11 Dec 2021 14:57:47: 14000000 INFO @ Sat, 11 Dec 2021 14:57:48: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:57:57: 15000000 INFO @ Sat, 11 Dec 2021 14:57:57: 12000000 INFO @ Sat, 11 Dec 2021 14:57:58: 18000000 INFO @ Sat, 11 Dec 2021 14:58:07: 16000000 INFO @ Sat, 11 Dec 2021 14:58:08: 13000000 INFO @ Sat, 11 Dec 2021 14:58:08: 19000000 INFO @ Sat, 11 Dec 2021 14:58:18: 17000000 INFO @ Sat, 11 Dec 2021 14:58:18: 20000000 INFO @ Sat, 11 Dec 2021 14:58:18: 14000000 INFO @ Sat, 11 Dec 2021 14:58:28: 21000000 INFO @ Sat, 11 Dec 2021 14:58:28: 18000000 INFO @ Sat, 11 Dec 2021 14:58:28: 15000000 INFO @ Sat, 11 Dec 2021 14:58:33: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:58:33: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:58:33: #1 total tags in treatment: 8569535 INFO @ Sat, 11 Dec 2021 14:58:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:58:33: #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 14:58:33: #1 tags after filtering in treatment: 6610101 INFO @ Sat, 11 Dec 2021 14:58:33: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 14:58:33: #1 finished! INFO @ Sat, 11 Dec 2021 14:58:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:58:34: #2 number of paired peaks: 1560 INFO @ Sat, 11 Dec 2021 14:58:34: start model_add_line... INFO @ Sat, 11 Dec 2021 14:58:34: start X-correlation... INFO @ Sat, 11 Dec 2021 14:58:34: end of X-cor INFO @ Sat, 11 Dec 2021 14:58:34: #2 finished! INFO @ Sat, 11 Dec 2021 14:58:34: #2 predicted fragment length is 82 bps INFO @ Sat, 11 Dec 2021 14:58:34: #2 alternative fragment length(s) may be 82 bps INFO @ Sat, 11 Dec 2021 14:58:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.05_model.r WARNING @ Sat, 11 Dec 2021 14:58:34: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:58:34: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Sat, 11 Dec 2021 14:58:34: #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 14:58:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:58:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:58:39: 19000000 INFO @ Sat, 11 Dec 2021 14:58:39: 16000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:58:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:58:49: 20000000 INFO @ Sat, 11 Dec 2021 14:58:50: 17000000 INFO @ Sat, 11 Dec 2021 14:58:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:58:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:58:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.05_summits.bed INFO @ Sat, 11 Dec 2021 14:58:58: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8579 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:59:00: 21000000 INFO @ Sat, 11 Dec 2021 14:59:01: 18000000 INFO @ Sat, 11 Dec 2021 14:59:05: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:59:05: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:59:05: #1 total tags in treatment: 8569535 INFO @ Sat, 11 Dec 2021 14:59:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:59:05: #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 14:59:06: #1 tags after filtering in treatment: 6610101 INFO @ Sat, 11 Dec 2021 14:59:06: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 14:59:06: #1 finished! INFO @ Sat, 11 Dec 2021 14:59:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:59:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:59:06: #2 number of paired peaks: 1560 INFO @ Sat, 11 Dec 2021 14:59:06: start model_add_line... INFO @ Sat, 11 Dec 2021 14:59:06: start X-correlation... INFO @ Sat, 11 Dec 2021 14:59:06: end of X-cor INFO @ Sat, 11 Dec 2021 14:59:06: #2 finished! INFO @ Sat, 11 Dec 2021 14:59:06: #2 predicted fragment length is 82 bps INFO @ Sat, 11 Dec 2021 14:59:06: #2 alternative fragment length(s) may be 82 bps INFO @ Sat, 11 Dec 2021 14:59:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.10_model.r WARNING @ Sat, 11 Dec 2021 14:59:06: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:59:06: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Sat, 11 Dec 2021 14:59:06: #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 14:59:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:59:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:59:11: 19000000 INFO @ Sat, 11 Dec 2021 14:59:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:59:21: 20000000 INFO @ Sat, 11 Dec 2021 14:59:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:59:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:59:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.10_summits.bed INFO @ Sat, 11 Dec 2021 14:59:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3877 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:59:32: 21000000 INFO @ Sat, 11 Dec 2021 14:59:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:59:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:59:38: #1 total tags in treatment: 8569535 INFO @ Sat, 11 Dec 2021 14:59:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:59:38: #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 14:59:38: #1 tags after filtering in treatment: 6610101 INFO @ Sat, 11 Dec 2021 14:59:38: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 14:59:38: #1 finished! INFO @ Sat, 11 Dec 2021 14:59:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:59:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:59:39: #2 number of paired peaks: 1560 INFO @ Sat, 11 Dec 2021 14:59:39: start model_add_line... INFO @ Sat, 11 Dec 2021 14:59:39: start X-correlation... INFO @ Sat, 11 Dec 2021 14:59:39: end of X-cor INFO @ Sat, 11 Dec 2021 14:59:39: #2 finished! INFO @ Sat, 11 Dec 2021 14:59:39: #2 predicted fragment length is 82 bps INFO @ Sat, 11 Dec 2021 14:59:39: #2 alternative fragment length(s) may be 82 bps INFO @ Sat, 11 Dec 2021 14:59:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.20_model.r WARNING @ Sat, 11 Dec 2021 14:59:39: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:59:39: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Sat, 11 Dec 2021 14:59:39: #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 14:59:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:59:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:59:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:00:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:00:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:00:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103815/SRX9103815.20_summits.bed INFO @ Sat, 11 Dec 2021 15:00:02: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (687 records, 4 fields): 4 millis CompletedMACS2peakCalling