Job ID = 14172000 SRX = SRX10089735 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21954335 spots for SRR13700622/SRR13700622.sra Written 21954335 spots for SRR13700622/SRR13700622.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172534 ("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: 00:25:45 21954335 reads; of these: 21954335 (100.00%) were paired; of these: 1772576 (8.07%) aligned concordantly 0 times 16305948 (74.27%) aligned concordantly exactly 1 time 3875811 (17.65%) aligned concordantly >1 times ---- 1772576 pairs aligned concordantly 0 times; of these: 177043 (9.99%) aligned discordantly 1 time ---- 1595533 pairs aligned 0 times concordantly or discordantly; of these: 3191066 mates make up the pairs; of these: 2437791 (76.39%) aligned 0 times 497686 (15.60%) aligned exactly 1 time 255589 (8.01%) aligned >1 times 94.45% overall alignment rate Time searching: 00:25:46 Overall time: 00:25:46 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] 2301860 / 14908309 = 0.1544 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 14:24:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.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 14:24:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:24:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:24:55: 1000000 INFO @ Sat, 11 Dec 2021 14:25:00: 2000000 INFO @ Sat, 11 Dec 2021 14:25:05: 3000000 INFO @ Sat, 11 Dec 2021 14:25:10: 4000000 INFO @ Sat, 11 Dec 2021 14:25:15: 5000000 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 14:25:19: 6000000 INFO @ Sat, 11 Dec 2021 14:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.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 14:25:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:25:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:25:24: 7000000 INFO @ Sat, 11 Dec 2021 14:25:25: 1000000 INFO @ Sat, 11 Dec 2021 14:25:29: 8000000 INFO @ Sat, 11 Dec 2021 14:25:30: 2000000 INFO @ Sat, 11 Dec 2021 14:25:34: 9000000 INFO @ Sat, 11 Dec 2021 14:25:35: 3000000 INFO @ Sat, 11 Dec 2021 14:25:39: 10000000 INFO @ Sat, 11 Dec 2021 14:25:40: 4000000 INFO @ Sat, 11 Dec 2021 14:25:44: 11000000 INFO @ Sat, 11 Dec 2021 14:25:45: 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 14:25:49: 12000000 INFO @ Sat, 11 Dec 2021 14:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.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 14:25:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:25:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:25:50: 6000000 INFO @ Sat, 11 Dec 2021 14:25:54: 13000000 INFO @ Sat, 11 Dec 2021 14:25:55: 7000000 INFO @ Sat, 11 Dec 2021 14:25:55: 1000000 INFO @ Sat, 11 Dec 2021 14:25:59: 14000000 INFO @ Sat, 11 Dec 2021 14:26:00: 8000000 INFO @ Sat, 11 Dec 2021 14:26:00: 2000000 INFO @ Sat, 11 Dec 2021 14:26:04: 15000000 INFO @ Sat, 11 Dec 2021 14:26:05: 9000000 INFO @ Sat, 11 Dec 2021 14:26:05: 3000000 INFO @ Sat, 11 Dec 2021 14:26:09: 16000000 INFO @ Sat, 11 Dec 2021 14:26:10: 10000000 INFO @ Sat, 11 Dec 2021 14:26:10: 4000000 INFO @ Sat, 11 Dec 2021 14:26:14: 17000000 INFO @ Sat, 11 Dec 2021 14:26:15: 11000000 INFO @ Sat, 11 Dec 2021 14:26:16: 5000000 INFO @ Sat, 11 Dec 2021 14:26:19: 18000000 INFO @ Sat, 11 Dec 2021 14:26:20: 12000000 INFO @ Sat, 11 Dec 2021 14:26:21: 6000000 INFO @ Sat, 11 Dec 2021 14:26:24: 19000000 INFO @ Sat, 11 Dec 2021 14:26:25: 13000000 INFO @ Sat, 11 Dec 2021 14:26:26: 7000000 INFO @ Sat, 11 Dec 2021 14:26:29: 20000000 INFO @ Sat, 11 Dec 2021 14:26:30: 14000000 INFO @ Sat, 11 Dec 2021 14:26:31: 8000000 INFO @ Sat, 11 Dec 2021 14:26:34: 21000000 INFO @ Sat, 11 Dec 2021 14:26:35: 15000000 INFO @ Sat, 11 Dec 2021 14:26:36: 9000000 INFO @ Sat, 11 Dec 2021 14:26:39: 22000000 INFO @ Sat, 11 Dec 2021 14:26:40: 16000000 INFO @ Sat, 11 Dec 2021 14:26:41: 10000000 INFO @ Sat, 11 Dec 2021 14:26:44: 23000000 INFO @ Sat, 11 Dec 2021 14:26:45: 17000000 INFO @ Sat, 11 Dec 2021 14:26:46: 11000000 INFO @ Sat, 11 Dec 2021 14:26:49: 24000000 INFO @ Sat, 11 Dec 2021 14:26:50: 18000000 INFO @ Sat, 11 Dec 2021 14:26:51: 12000000 INFO @ Sat, 11 Dec 2021 14:26:54: 25000000 INFO @ Sat, 11 Dec 2021 14:26:55: 19000000 INFO @ Sat, 11 Dec 2021 14:26:56: 13000000 INFO @ Sat, 11 Dec 2021 14:26:59: 26000000 INFO @ Sat, 11 Dec 2021 14:27:00: 20000000 INFO @ Sat, 11 Dec 2021 14:27:01: 14000000 INFO @ Sat, 11 Dec 2021 14:27:05: 27000000 INFO @ Sat, 11 Dec 2021 14:27:05: 21000000 INFO @ Sat, 11 Dec 2021 14:27:06: 15000000 INFO @ Sat, 11 Dec 2021 14:27:09: 28000000 INFO @ Sat, 11 Dec 2021 14:27:10: 22000000 INFO @ Sat, 11 Dec 2021 14:27:11: 16000000 INFO @ Sat, 11 Dec 2021 14:27:14: 29000000 INFO @ Sat, 11 Dec 2021 14:27:16: 23000000 INFO @ Sat, 11 Dec 2021 14:27:16: 17000000 INFO @ Sat, 11 Dec 2021 14:27:19: 30000000 INFO @ Sat, 11 Dec 2021 14:27:21: 24000000 INFO @ Sat, 11 Dec 2021 14:27:21: 18000000 INFO @ Sat, 11 Dec 2021 14:27:24: 31000000 INFO @ Sat, 11 Dec 2021 14:27:26: 25000000 INFO @ Sat, 11 Dec 2021 14:27:26: 19000000 INFO @ Sat, 11 Dec 2021 14:27:29: 32000000 INFO @ Sat, 11 Dec 2021 14:27:31: 26000000 INFO @ Sat, 11 Dec 2021 14:27:31: 20000000 INFO @ Sat, 11 Dec 2021 14:27:34: 33000000 INFO @ Sat, 11 Dec 2021 14:27:36: 27000000 INFO @ Sat, 11 Dec 2021 14:27:36: 21000000 INFO @ Sat, 11 Dec 2021 14:27:39: 34000000 INFO @ Sat, 11 Dec 2021 14:27:41: 28000000 INFO @ Sat, 11 Dec 2021 14:27:41: 22000000 INFO @ Sat, 11 Dec 2021 14:27:44: 35000000 INFO @ Sat, 11 Dec 2021 14:27:45: 29000000 INFO @ Sat, 11 Dec 2021 14:27:46: 23000000 INFO @ Sat, 11 Dec 2021 14:27:49: 36000000 INFO @ Sat, 11 Dec 2021 14:27:50: 30000000 INFO @ Sat, 11 Dec 2021 14:27:51: 24000000 INFO @ Sat, 11 Dec 2021 14:27:54: #1 tag size is determined as 68 bps INFO @ Sat, 11 Dec 2021 14:27:54: #1 tag size = 68 INFO @ Sat, 11 Dec 2021 14:27:54: #1 total tags in treatment: 17881997 INFO @ Sat, 11 Dec 2021 14:27:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:27:54: #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 14:27:54: #1 tags after filtering in treatment: 11137376 INFO @ Sat, 11 Dec 2021 14:27:54: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 14:27:54: #1 finished! INFO @ Sat, 11 Dec 2021 14:27:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:27:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:27:55: #2 number of paired peaks: 2982 INFO @ Sat, 11 Dec 2021 14:27:55: start model_add_line... INFO @ Sat, 11 Dec 2021 14:27:55: start X-correlation... INFO @ Sat, 11 Dec 2021 14:27:55: end of X-cor INFO @ Sat, 11 Dec 2021 14:27:55: #2 finished! INFO @ Sat, 11 Dec 2021 14:27:55: #2 predicted fragment length is 93 bps INFO @ Sat, 11 Dec 2021 14:27:55: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 11 Dec 2021 14:27:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.05_model.r WARNING @ Sat, 11 Dec 2021 14:27:55: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:27:55: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 11 Dec 2021 14:27:55: #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 14:27:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:27:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:27:56: 31000000 INFO @ Sat, 11 Dec 2021 14:27:56: 25000000 INFO @ Sat, 11 Dec 2021 14:28:01: 32000000 INFO @ Sat, 11 Dec 2021 14:28:01: 26000000 INFO @ Sat, 11 Dec 2021 14:28:06: 33000000 INFO @ Sat, 11 Dec 2021 14:28:06: 27000000 INFO @ Sat, 11 Dec 2021 14:28:11: 34000000 INFO @ Sat, 11 Dec 2021 14:28:11: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:28:15: 35000000 INFO @ Sat, 11 Dec 2021 14:28:16: 29000000 INFO @ Sat, 11 Dec 2021 14:28:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:28:20: 36000000 INFO @ Sat, 11 Dec 2021 14:28:21: 30000000 INFO @ Sat, 11 Dec 2021 14:28:25: #1 tag size is determined as 68 bps INFO @ Sat, 11 Dec 2021 14:28:25: #1 tag size = 68 INFO @ Sat, 11 Dec 2021 14:28:25: #1 total tags in treatment: 17881997 INFO @ Sat, 11 Dec 2021 14:28:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:28:25: #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 14:28:25: #1 tags after filtering in treatment: 11137376 INFO @ Sat, 11 Dec 2021 14:28:25: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 14:28:25: #1 finished! INFO @ Sat, 11 Dec 2021 14:28:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:28:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:28:26: 31000000 INFO @ Sat, 11 Dec 2021 14:28:26: #2 number of paired peaks: 2982 INFO @ Sat, 11 Dec 2021 14:28:26: start model_add_line... INFO @ Sat, 11 Dec 2021 14:28:26: start X-correlation... INFO @ Sat, 11 Dec 2021 14:28:26: end of X-cor INFO @ Sat, 11 Dec 2021 14:28:26: #2 finished! INFO @ Sat, 11 Dec 2021 14:28:26: #2 predicted fragment length is 93 bps INFO @ Sat, 11 Dec 2021 14:28:26: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 11 Dec 2021 14:28:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.10_model.r WARNING @ Sat, 11 Dec 2021 14:28:26: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:28:26: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 11 Dec 2021 14:28:26: #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 14:28:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:28:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:28:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:28:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:28:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.05_summits.bed INFO @ Sat, 11 Dec 2021 14:28:30: Done! pass1 - making usageList (15 chroms): 3 millis INFO @ Sat, 11 Dec 2021 14:28:30: 32000000 pass2 - checking and writing primary data (17524 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:28:35: 33000000 INFO @ Sat, 11 Dec 2021 14:28:40: 34000000 INFO @ Sat, 11 Dec 2021 14:28:45: 35000000 INFO @ Sat, 11 Dec 2021 14:28:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:28:50: 36000000 INFO @ Sat, 11 Dec 2021 14:28:54: #1 tag size is determined as 68 bps INFO @ Sat, 11 Dec 2021 14:28:54: #1 tag size = 68 INFO @ Sat, 11 Dec 2021 14:28:54: #1 total tags in treatment: 17881997 INFO @ Sat, 11 Dec 2021 14:28:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:28:54: #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 14:28:55: #1 tags after filtering in treatment: 11137376 INFO @ Sat, 11 Dec 2021 14:28:55: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 14:28:55: #1 finished! INFO @ Sat, 11 Dec 2021 14:28:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:28:56: #2 number of paired peaks: 2982 INFO @ Sat, 11 Dec 2021 14:28:56: start model_add_line... INFO @ Sat, 11 Dec 2021 14:28:56: start X-correlation... INFO @ Sat, 11 Dec 2021 14:28:56: end of X-cor INFO @ Sat, 11 Dec 2021 14:28:56: #2 finished! INFO @ Sat, 11 Dec 2021 14:28:56: #2 predicted fragment length is 93 bps INFO @ Sat, 11 Dec 2021 14:28:56: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 11 Dec 2021 14:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.20_model.r WARNING @ Sat, 11 Dec 2021 14:28:56: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:28:56: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 11 Dec 2021 14:28:56: #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 14:28:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:28:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:28:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:28:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.10_summits.bed INFO @ Sat, 11 Dec 2021 14:29:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11488 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:29:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:29:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:29:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:29:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089735/SRX10089735.20_summits.bed INFO @ Sat, 11 Dec 2021 14:29:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4923 records, 4 fields): 6 millis CompletedMACS2peakCalling