Job ID = 12265259 SRX = SRX4664638 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27344125 spots for SRR7813065/SRR7813065.sra Written 27344125 spots for SRR7813065/SRR7813065.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265602 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:55:28 27344125 reads; of these: 27344125 (100.00%) were paired; of these: 7831302 (28.64%) aligned concordantly 0 times 10192347 (37.27%) aligned concordantly exactly 1 time 9320476 (34.09%) aligned concordantly >1 times ---- 7831302 pairs aligned concordantly 0 times; of these: 2301818 (29.39%) aligned discordantly 1 time ---- 5529484 pairs aligned 0 times concordantly or discordantly; of these: 11058968 mates make up the pairs; of these: 7411593 (67.02%) aligned 0 times 956423 (8.65%) aligned exactly 1 time 2690952 (24.33%) aligned >1 times 86.45% overall alignment rate Time searching: 00:55:29 Overall time: 00:55:29 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] 5952364 / 21503766 = 0.2768 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:31:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.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, 03 Apr 2021 07:31:03: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:31:03: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:31:09: 1000000 INFO @ Sat, 03 Apr 2021 07:31:16: 2000000 INFO @ Sat, 03 Apr 2021 07:31:22: 3000000 INFO @ Sat, 03 Apr 2021 07:31:28: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:31:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.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, 03 Apr 2021 07:31:33: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:31:33: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:31:34: 5000000 INFO @ Sat, 03 Apr 2021 07:31:40: 1000000 INFO @ Sat, 03 Apr 2021 07:31:41: 6000000 INFO @ Sat, 03 Apr 2021 07:31:46: 2000000 INFO @ Sat, 03 Apr 2021 07:31:47: 7000000 INFO @ Sat, 03 Apr 2021 07:31:52: 3000000 INFO @ Sat, 03 Apr 2021 07:31:54: 8000000 INFO @ Sat, 03 Apr 2021 07:31:59: 4000000 INFO @ Sat, 03 Apr 2021 07:32:00: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:32:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.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, 03 Apr 2021 07:32:03: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:32:03: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:32:05: 5000000 INFO @ Sat, 03 Apr 2021 07:32:06: 10000000 INFO @ Sat, 03 Apr 2021 07:32:10: 1000000 INFO @ Sat, 03 Apr 2021 07:32:12: 6000000 INFO @ Sat, 03 Apr 2021 07:32:14: 11000000 INFO @ Sat, 03 Apr 2021 07:32:18: 2000000 INFO @ Sat, 03 Apr 2021 07:32:20: 7000000 INFO @ Sat, 03 Apr 2021 07:32:21: 12000000 INFO @ Sat, 03 Apr 2021 07:32:25: 3000000 INFO @ Sat, 03 Apr 2021 07:32:27: 8000000 INFO @ Sat, 03 Apr 2021 07:32:28: 13000000 INFO @ Sat, 03 Apr 2021 07:32:32: 4000000 INFO @ Sat, 03 Apr 2021 07:32:35: 9000000 INFO @ Sat, 03 Apr 2021 07:32:35: 14000000 INFO @ Sat, 03 Apr 2021 07:32:39: 5000000 INFO @ Sat, 03 Apr 2021 07:32:42: 10000000 INFO @ Sat, 03 Apr 2021 07:32:42: 15000000 INFO @ Sat, 03 Apr 2021 07:32:46: 6000000 INFO @ Sat, 03 Apr 2021 07:32:49: 11000000 INFO @ Sat, 03 Apr 2021 07:32:50: 16000000 INFO @ Sat, 03 Apr 2021 07:32:54: 7000000 INFO @ Sat, 03 Apr 2021 07:32:57: 12000000 INFO @ Sat, 03 Apr 2021 07:32:57: 17000000 INFO @ Sat, 03 Apr 2021 07:33:01: 8000000 INFO @ Sat, 03 Apr 2021 07:33:04: 13000000 INFO @ Sat, 03 Apr 2021 07:33:04: 18000000 INFO @ Sat, 03 Apr 2021 07:33:08: 9000000 INFO @ Sat, 03 Apr 2021 07:33:11: 14000000 INFO @ Sat, 03 Apr 2021 07:33:11: 19000000 INFO @ Sat, 03 Apr 2021 07:33:16: 10000000 INFO @ Sat, 03 Apr 2021 07:33:18: 15000000 INFO @ Sat, 03 Apr 2021 07:33:19: 20000000 INFO @ Sat, 03 Apr 2021 07:33:22: 11000000 INFO @ Sat, 03 Apr 2021 07:33:25: 16000000 INFO @ Sat, 03 Apr 2021 07:33:26: 21000000 INFO @ Sat, 03 Apr 2021 07:33:29: 12000000 INFO @ Sat, 03 Apr 2021 07:33:33: 17000000 INFO @ Sat, 03 Apr 2021 07:33:33: 22000000 INFO @ Sat, 03 Apr 2021 07:33:36: 13000000 INFO @ Sat, 03 Apr 2021 07:33:40: 23000000 INFO @ Sat, 03 Apr 2021 07:33:40: 18000000 INFO @ Sat, 03 Apr 2021 07:33:44: 14000000 INFO @ Sat, 03 Apr 2021 07:33:46: 24000000 INFO @ Sat, 03 Apr 2021 07:33:47: 19000000 INFO @ Sat, 03 Apr 2021 07:33:51: 15000000 INFO @ Sat, 03 Apr 2021 07:33:53: 25000000 INFO @ Sat, 03 Apr 2021 07:33:54: 20000000 INFO @ Sat, 03 Apr 2021 07:33:58: 16000000 INFO @ Sat, 03 Apr 2021 07:34:00: 26000000 INFO @ Sat, 03 Apr 2021 07:34:02: 21000000 INFO @ Sat, 03 Apr 2021 07:34:06: 17000000 INFO @ Sat, 03 Apr 2021 07:34:08: 27000000 INFO @ Sat, 03 Apr 2021 07:34:10: 22000000 INFO @ Sat, 03 Apr 2021 07:34:14: 18000000 INFO @ Sat, 03 Apr 2021 07:34:15: 28000000 INFO @ Sat, 03 Apr 2021 07:34:17: 23000000 INFO @ Sat, 03 Apr 2021 07:34:21: 19000000 INFO @ Sat, 03 Apr 2021 07:34:23: 29000000 INFO @ Sat, 03 Apr 2021 07:34:25: 24000000 INFO @ Sat, 03 Apr 2021 07:34:29: 20000000 INFO @ Sat, 03 Apr 2021 07:34:31: 30000000 INFO @ Sat, 03 Apr 2021 07:34:32: 25000000 INFO @ Sat, 03 Apr 2021 07:34:36: 21000000 INFO @ Sat, 03 Apr 2021 07:34:38: 31000000 INFO @ Sat, 03 Apr 2021 07:34:39: 26000000 INFO @ Sat, 03 Apr 2021 07:34:44: 22000000 INFO @ Sat, 03 Apr 2021 07:34:45: 32000000 INFO @ Sat, 03 Apr 2021 07:34:46: 27000000 INFO @ Sat, 03 Apr 2021 07:34:51: 23000000 INFO @ Sat, 03 Apr 2021 07:34:53: 33000000 INFO @ Sat, 03 Apr 2021 07:34:54: 28000000 INFO @ Sat, 03 Apr 2021 07:34:58: 24000000 INFO @ Sat, 03 Apr 2021 07:35:00: 34000000 INFO @ Sat, 03 Apr 2021 07:35:01: 29000000 INFO @ Sat, 03 Apr 2021 07:35:04: 25000000 INFO @ Sat, 03 Apr 2021 07:35:07: 35000000 INFO @ Sat, 03 Apr 2021 07:35:08: 30000000 INFO @ Sat, 03 Apr 2021 07:35:10: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:35:10: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:35:10: #1 total tags in treatment: 13910081 INFO @ Sat, 03 Apr 2021 07:35:10: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:35:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:35:10: #1 tags after filtering in treatment: 10214057 INFO @ Sat, 03 Apr 2021 07:35:10: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:35:10: #1 finished! INFO @ Sat, 03 Apr 2021 07:35:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:35:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:35:11: #2 number of paired peaks: 1446 INFO @ Sat, 03 Apr 2021 07:35:11: start model_add_line... INFO @ Sat, 03 Apr 2021 07:35:11: 26000000 INFO @ Sat, 03 Apr 2021 07:35:11: start X-correlation... INFO @ Sat, 03 Apr 2021 07:35:11: end of X-cor INFO @ Sat, 03 Apr 2021 07:35:11: #2 finished! INFO @ Sat, 03 Apr 2021 07:35:11: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 07:35:11: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 07:35:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.05_model.r WARNING @ Sat, 03 Apr 2021 07:35:11: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:35:11: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 07:35:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:35:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:35:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:35:14: 31000000 INFO @ Sat, 03 Apr 2021 07:35:17: 27000000 INFO @ Sat, 03 Apr 2021 07:35:21: 32000000 INFO @ Sat, 03 Apr 2021 07:35:23: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:35:27: 33000000 INFO @ Sat, 03 Apr 2021 07:35:30: 29000000 INFO @ Sat, 03 Apr 2021 07:35:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:35:34: 34000000 INFO @ Sat, 03 Apr 2021 07:35:36: 30000000 INFO @ Sat, 03 Apr 2021 07:35:41: 35000000 INFO @ Sat, 03 Apr 2021 07:35:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:35:43: 31000000 INFO @ Sat, 03 Apr 2021 07:35:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:35:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.05_summits.bed INFO @ Sat, 03 Apr 2021 07:35:43: Done! INFO @ Sat, 03 Apr 2021 07:35:43: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:35:43: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:35:43: #1 total tags in treatment: 13910081 INFO @ Sat, 03 Apr 2021 07:35:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:35:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10774 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:35:44: #1 tags after filtering in treatment: 10214057 INFO @ Sat, 03 Apr 2021 07:35:44: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:35:44: #1 finished! INFO @ Sat, 03 Apr 2021 07:35:44: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:35:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:35:44: #2 number of paired peaks: 1446 INFO @ Sat, 03 Apr 2021 07:35:44: start model_add_line... INFO @ Sat, 03 Apr 2021 07:35:45: start X-correlation... INFO @ Sat, 03 Apr 2021 07:35:45: end of X-cor INFO @ Sat, 03 Apr 2021 07:35:45: #2 finished! INFO @ Sat, 03 Apr 2021 07:35:45: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 07:35:45: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 07:35:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.10_model.r WARNING @ Sat, 03 Apr 2021 07:35:45: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:35:45: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 07:35:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:35:45: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:35:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:35:49: 32000000 INFO @ Sat, 03 Apr 2021 07:35:55: 33000000 INFO @ Sat, 03 Apr 2021 07:36:01: 34000000 INFO @ Sat, 03 Apr 2021 07:36:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:36:07: 35000000 INFO @ Sat, 03 Apr 2021 07:36:10: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:36:10: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:36:10: #1 total tags in treatment: 13910081 INFO @ Sat, 03 Apr 2021 07:36:10: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:36:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:36:10: #1 tags after filtering in treatment: 10214057 INFO @ Sat, 03 Apr 2021 07:36:10: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:36:10: #1 finished! INFO @ Sat, 03 Apr 2021 07:36:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:36:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:36:11: #2 number of paired peaks: 1446 INFO @ Sat, 03 Apr 2021 07:36:11: start model_add_line... INFO @ Sat, 03 Apr 2021 07:36:11: start X-correlation... INFO @ Sat, 03 Apr 2021 07:36:11: end of X-cor INFO @ Sat, 03 Apr 2021 07:36:11: #2 finished! INFO @ Sat, 03 Apr 2021 07:36:11: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 07:36:11: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 07:36:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.20_model.r WARNING @ Sat, 03 Apr 2021 07:36:11: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:36:11: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 07:36:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:36:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:36:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:36:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:36:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:36:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.10_summits.bed INFO @ Sat, 03 Apr 2021 07:36:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4778 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:36:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:36:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:36:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:36:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664638/SRX4664638.20_summits.bed INFO @ Sat, 03 Apr 2021 07:36:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1200 records, 4 fields): 3 millis CompletedMACS2peakCalling