Job ID = 16439376 SRX = SRX14232186 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20645039 spots for SRR18080632/SRR18080632.sra Written 20645039 spots for SRR18080632/SRR18080632.sra fastq に変換しました。 bowtie でマッピング中... Your job 16441923 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 05:07:52 20645039 reads; of these: 20645039 (100.00%) were paired; of these: 6653411 (32.23%) aligned concordantly 0 times 5626662 (27.25%) aligned concordantly exactly 1 time 8364966 (40.52%) aligned concordantly >1 times ---- 6653411 pairs aligned concordantly 0 times; of these: 1182319 (17.77%) aligned discordantly 1 time ---- 5471092 pairs aligned 0 times concordantly or discordantly; of these: 10942184 mates make up the pairs; of these: 7269070 (66.43%) aligned 0 times 358205 (3.27%) aligned exactly 1 time 3314909 (30.29%) aligned >1 times 82.40% overall alignment rate Time searching: 05:07:54 Overall time: 05:07:54 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 28 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] 4300666 / 14958490 = 0.2875 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 20:30:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.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 @ Tue, 02 Aug 2022 20:30:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 20:30:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 20:30:54: 1000000 INFO @ Tue, 02 Aug 2022 20:31:05: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 20:31:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.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 @ Tue, 02 Aug 2022 20:31:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 20:31:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 20:31:18: 3000000 INFO @ Tue, 02 Aug 2022 20:31:26: 1000000 INFO @ Tue, 02 Aug 2022 20:31:31: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 20:31:42: 2000000 INFO @ Tue, 02 Aug 2022 20:31:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.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 @ Tue, 02 Aug 2022 20:31:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 20:31:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 20:31:45: 5000000 INFO @ Tue, 02 Aug 2022 20:31:57: 3000000 INFO @ Tue, 02 Aug 2022 20:31:58: 1000000 INFO @ Tue, 02 Aug 2022 20:32:01: 6000000 INFO @ Tue, 02 Aug 2022 20:32:11: 2000000 INFO @ Tue, 02 Aug 2022 20:32:11: 4000000 INFO @ Tue, 02 Aug 2022 20:32:15: 7000000 INFO @ Tue, 02 Aug 2022 20:32:24: 3000000 INFO @ Tue, 02 Aug 2022 20:32:25: 5000000 INFO @ Tue, 02 Aug 2022 20:32:30: 8000000 INFO @ Tue, 02 Aug 2022 20:32:37: 4000000 INFO @ Tue, 02 Aug 2022 20:32:39: 6000000 INFO @ Tue, 02 Aug 2022 20:32:42: 9000000 INFO @ Tue, 02 Aug 2022 20:32:49: 5000000 INFO @ Tue, 02 Aug 2022 20:32:51: 7000000 INFO @ Tue, 02 Aug 2022 20:32:54: 10000000 INFO @ Tue, 02 Aug 2022 20:33:01: 6000000 INFO @ Tue, 02 Aug 2022 20:33:03: 8000000 INFO @ Tue, 02 Aug 2022 20:33:05: 11000000 INFO @ Tue, 02 Aug 2022 20:33:13: 7000000 INFO @ Tue, 02 Aug 2022 20:33:15: 9000000 INFO @ Tue, 02 Aug 2022 20:33:17: 12000000 INFO @ Tue, 02 Aug 2022 20:33:25: 8000000 INFO @ Tue, 02 Aug 2022 20:33:27: 10000000 INFO @ Tue, 02 Aug 2022 20:33:29: 13000000 INFO @ Tue, 02 Aug 2022 20:33:37: 9000000 INFO @ Tue, 02 Aug 2022 20:33:39: 11000000 INFO @ Tue, 02 Aug 2022 20:33:40: 14000000 INFO @ Tue, 02 Aug 2022 20:33:49: 10000000 INFO @ Tue, 02 Aug 2022 20:33:50: 12000000 INFO @ Tue, 02 Aug 2022 20:33:53: 15000000 INFO @ Tue, 02 Aug 2022 20:34:02: 11000000 INFO @ Tue, 02 Aug 2022 20:34:02: 13000000 INFO @ Tue, 02 Aug 2022 20:34:05: 16000000 INFO @ Tue, 02 Aug 2022 20:34:13: 12000000 INFO @ Tue, 02 Aug 2022 20:34:14: 14000000 INFO @ Tue, 02 Aug 2022 20:34:16: 17000000 INFO @ Tue, 02 Aug 2022 20:34:26: 13000000 INFO @ Tue, 02 Aug 2022 20:34:26: 15000000 INFO @ Tue, 02 Aug 2022 20:34:27: 18000000 INFO @ Tue, 02 Aug 2022 20:34:37: 16000000 INFO @ Tue, 02 Aug 2022 20:34:37: 14000000 INFO @ Tue, 02 Aug 2022 20:34:39: 19000000 INFO @ Tue, 02 Aug 2022 20:34:49: 17000000 INFO @ Tue, 02 Aug 2022 20:34:50: 15000000 INFO @ Tue, 02 Aug 2022 20:34:50: 20000000 INFO @ Tue, 02 Aug 2022 20:35:02: 18000000 INFO @ Tue, 02 Aug 2022 20:35:02: 21000000 INFO @ Tue, 02 Aug 2022 20:35:02: 16000000 INFO @ Tue, 02 Aug 2022 20:35:14: 22000000 INFO @ Tue, 02 Aug 2022 20:35:15: 19000000 INFO @ Tue, 02 Aug 2022 20:35:15: 17000000 INFO @ Tue, 02 Aug 2022 20:35:26: 23000000 INFO @ Tue, 02 Aug 2022 20:35:27: 18000000 INFO @ Tue, 02 Aug 2022 20:35:27: 20000000 INFO @ Tue, 02 Aug 2022 20:35:38: 19000000 INFO @ Tue, 02 Aug 2022 20:35:39: 21000000 INFO @ Tue, 02 Aug 2022 20:35:39: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 20:35:50: 20000000 INFO @ Tue, 02 Aug 2022 20:35:50: 22000000 INFO @ Tue, 02 Aug 2022 20:35:52: 25000000 INFO @ Tue, 02 Aug 2022 20:35:57: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 20:35:57: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 20:35:57: #1 total tags in treatment: 9910259 INFO @ Tue, 02 Aug 2022 20:35:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 20:35:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 20:35:57: #1 tags after filtering in treatment: 6565543 INFO @ Tue, 02 Aug 2022 20:35:57: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 02 Aug 2022 20:35:57: #1 finished! INFO @ Tue, 02 Aug 2022 20:35:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 20:35:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 20:35:58: #2 number of paired peaks: 3034 INFO @ Tue, 02 Aug 2022 20:35:58: start model_add_line... INFO @ Tue, 02 Aug 2022 20:35:58: start X-correlation... INFO @ Tue, 02 Aug 2022 20:35:58: end of X-cor INFO @ Tue, 02 Aug 2022 20:35:58: #2 finished! INFO @ Tue, 02 Aug 2022 20:35:58: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 20:35:58: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 20:35:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.05_model.r WARNING @ Tue, 02 Aug 2022 20:35:58: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 20:35:58: #2 You may need to consider one of the other alternative d(s): 175 WARNING @ Tue, 02 Aug 2022 20:35:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 20:35:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 20:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 20:36:02: 21000000 INFO @ Tue, 02 Aug 2022 20:36:03: 23000000 INFO @ Tue, 02 Aug 2022 20:36:14: 22000000 INFO @ Tue, 02 Aug 2022 20:36:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 20:36:17: 24000000 INFO @ Tue, 02 Aug 2022 20:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.05_peaks.xls INFO @ Tue, 02 Aug 2022 20:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 20:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.05_summits.bed INFO @ Tue, 02 Aug 2022 20:36:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4895 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 20:36:27: 23000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 20:36:29: 25000000 INFO @ Tue, 02 Aug 2022 20:36:34: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 20:36:34: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 20:36:34: #1 total tags in treatment: 9910259 INFO @ Tue, 02 Aug 2022 20:36:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 20:36:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 20:36:34: #1 tags after filtering in treatment: 6565543 INFO @ Tue, 02 Aug 2022 20:36:34: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 02 Aug 2022 20:36:34: #1 finished! INFO @ Tue, 02 Aug 2022 20:36:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 20:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 20:36:35: #2 number of paired peaks: 3034 INFO @ Tue, 02 Aug 2022 20:36:35: start model_add_line... INFO @ Tue, 02 Aug 2022 20:36:35: start X-correlation... INFO @ Tue, 02 Aug 2022 20:36:35: end of X-cor INFO @ Tue, 02 Aug 2022 20:36:35: #2 finished! INFO @ Tue, 02 Aug 2022 20:36:35: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 20:36:35: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 20:36:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.10_model.r WARNING @ Tue, 02 Aug 2022 20:36:35: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 20:36:35: #2 You may need to consider one of the other alternative d(s): 175 WARNING @ Tue, 02 Aug 2022 20:36:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 20:36:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 20:36:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 20:36:40: 24000000 INFO @ Tue, 02 Aug 2022 20:36:52: 25000000 INFO @ Tue, 02 Aug 2022 20:36:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 20:36:56: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 20:36:56: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 20:36:56: #1 total tags in treatment: 9910259 INFO @ Tue, 02 Aug 2022 20:36:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 20:36:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 20:36:57: #1 tags after filtering in treatment: 6565543 INFO @ Tue, 02 Aug 2022 20:36:57: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 02 Aug 2022 20:36:57: #1 finished! INFO @ Tue, 02 Aug 2022 20:36:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 20:36:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 20:36:57: #2 number of paired peaks: 3034 INFO @ Tue, 02 Aug 2022 20:36:57: start model_add_line... INFO @ Tue, 02 Aug 2022 20:36:57: start X-correlation... INFO @ Tue, 02 Aug 2022 20:36:57: end of X-cor INFO @ Tue, 02 Aug 2022 20:36:57: #2 finished! INFO @ Tue, 02 Aug 2022 20:36:57: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 20:36:57: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 20:36:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.20_model.r WARNING @ Tue, 02 Aug 2022 20:36:57: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 20:36:57: #2 You may need to consider one of the other alternative d(s): 175 WARNING @ Tue, 02 Aug 2022 20:36:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 20:36:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 20:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 20:36:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.10_peaks.xls INFO @ Tue, 02 Aug 2022 20:36:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 20:36:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.10_summits.bed INFO @ Tue, 02 Aug 2022 20:36:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3881 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 20:37:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 20:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.20_peaks.xls INFO @ Tue, 02 Aug 2022 20:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 20:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232186/SRX14232186.20_summits.bed INFO @ Tue, 02 Aug 2022 20:37:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3178 records, 4 fields): 8 millis CompletedMACS2peakCalling