Job ID = 14167055 SRX = SRX9343229 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18731911 spots for SRR12877205/SRR12877205.sra Written 18731911 spots for SRR12877205/SRR12877205.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167502 ("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: 00:23:06 18731911 reads; of these: 18731911 (100.00%) were paired; of these: 5728123 (30.58%) aligned concordantly 0 times 10729120 (57.28%) aligned concordantly exactly 1 time 2274668 (12.14%) aligned concordantly >1 times ---- 5728123 pairs aligned concordantly 0 times; of these: 1598631 (27.91%) aligned discordantly 1 time ---- 4129492 pairs aligned 0 times concordantly or discordantly; of these: 8258984 mates make up the pairs; of these: 7095466 (85.91%) aligned 0 times 485525 (5.88%) aligned exactly 1 time 677993 (8.21%) aligned >1 times 81.06% overall alignment rate Time searching: 00:23:06 Overall time: 00:23:06 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] 1052212 / 14493383 = 0.0726 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 09:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.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 09:59:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:59:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:59:33: 1000000 INFO @ Fri, 10 Dec 2021 09:59:39: 2000000 INFO @ Fri, 10 Dec 2021 09:59:46: 3000000 INFO @ Fri, 10 Dec 2021 09:59:52: 4000000 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 09:59:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.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 09:59:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:59:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:59:58: 5000000 INFO @ Fri, 10 Dec 2021 10:00:02: 1000000 INFO @ Fri, 10 Dec 2021 10:00:05: 6000000 INFO @ Fri, 10 Dec 2021 10:00:09: 2000000 INFO @ Fri, 10 Dec 2021 10:00:12: 7000000 INFO @ Fri, 10 Dec 2021 10:00:16: 3000000 INFO @ Fri, 10 Dec 2021 10:00:19: 8000000 INFO @ Fri, 10 Dec 2021 10:00:23: 4000000 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 10:00:26: 9000000 INFO @ Fri, 10 Dec 2021 10:00:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.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 10:00:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:00:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:00:30: 5000000 INFO @ Fri, 10 Dec 2021 10:00:32: 10000000 INFO @ Fri, 10 Dec 2021 10:00:33: 1000000 INFO @ Fri, 10 Dec 2021 10:00:37: 6000000 INFO @ Fri, 10 Dec 2021 10:00:39: 11000000 INFO @ Fri, 10 Dec 2021 10:00:40: 2000000 INFO @ Fri, 10 Dec 2021 10:00:44: 7000000 INFO @ Fri, 10 Dec 2021 10:00:46: 12000000 INFO @ Fri, 10 Dec 2021 10:00:46: 3000000 INFO @ Fri, 10 Dec 2021 10:00:51: 8000000 INFO @ Fri, 10 Dec 2021 10:00:53: 13000000 INFO @ Fri, 10 Dec 2021 10:00:53: 4000000 INFO @ Fri, 10 Dec 2021 10:00:58: 9000000 INFO @ Fri, 10 Dec 2021 10:00:59: 14000000 INFO @ Fri, 10 Dec 2021 10:01:00: 5000000 INFO @ Fri, 10 Dec 2021 10:01:05: 10000000 INFO @ Fri, 10 Dec 2021 10:01:06: 15000000 INFO @ Fri, 10 Dec 2021 10:01:07: 6000000 INFO @ Fri, 10 Dec 2021 10:01:12: 11000000 INFO @ Fri, 10 Dec 2021 10:01:13: 16000000 INFO @ Fri, 10 Dec 2021 10:01:14: 7000000 INFO @ Fri, 10 Dec 2021 10:01:19: 12000000 INFO @ Fri, 10 Dec 2021 10:01:20: 17000000 INFO @ Fri, 10 Dec 2021 10:01:21: 8000000 INFO @ Fri, 10 Dec 2021 10:01:26: 13000000 INFO @ Fri, 10 Dec 2021 10:01:26: 18000000 INFO @ Fri, 10 Dec 2021 10:01:28: 9000000 INFO @ Fri, 10 Dec 2021 10:01:32: 14000000 INFO @ Fri, 10 Dec 2021 10:01:33: 19000000 INFO @ Fri, 10 Dec 2021 10:01:35: 10000000 INFO @ Fri, 10 Dec 2021 10:01:39: 15000000 INFO @ Fri, 10 Dec 2021 10:01:40: 20000000 INFO @ Fri, 10 Dec 2021 10:01:42: 11000000 INFO @ Fri, 10 Dec 2021 10:01:46: 16000000 INFO @ Fri, 10 Dec 2021 10:01:47: 21000000 INFO @ Fri, 10 Dec 2021 10:01:49: 12000000 INFO @ Fri, 10 Dec 2021 10:01:53: 17000000 INFO @ Fri, 10 Dec 2021 10:01:53: 22000000 INFO @ Fri, 10 Dec 2021 10:01:56: 13000000 INFO @ Fri, 10 Dec 2021 10:02:00: 18000000 INFO @ Fri, 10 Dec 2021 10:02:00: 23000000 INFO @ Fri, 10 Dec 2021 10:02:02: 14000000 INFO @ Fri, 10 Dec 2021 10:02:07: 19000000 INFO @ Fri, 10 Dec 2021 10:02:07: 24000000 INFO @ Fri, 10 Dec 2021 10:02:09: 15000000 INFO @ Fri, 10 Dec 2021 10:02:14: 20000000 INFO @ Fri, 10 Dec 2021 10:02:14: 25000000 INFO @ Fri, 10 Dec 2021 10:02:16: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:02:21: 21000000 INFO @ Fri, 10 Dec 2021 10:02:21: 26000000 INFO @ Fri, 10 Dec 2021 10:02:24: 17000000 INFO @ Fri, 10 Dec 2021 10:02:28: 22000000 INFO @ Fri, 10 Dec 2021 10:02:28: 27000000 INFO @ Fri, 10 Dec 2021 10:02:31: 18000000 INFO @ Fri, 10 Dec 2021 10:02:36: 28000000 INFO @ Fri, 10 Dec 2021 10:02:36: 23000000 INFO @ Fri, 10 Dec 2021 10:02:37: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:02:37: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:02:37: #1 total tags in treatment: 12044493 INFO @ Fri, 10 Dec 2021 10:02:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:02:37: #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 10:02:38: #1 tags after filtering in treatment: 9607618 INFO @ Fri, 10 Dec 2021 10:02:38: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 10 Dec 2021 10:02:38: #1 finished! INFO @ Fri, 10 Dec 2021 10:02:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:02:38: #2 number of paired peaks: 1027 INFO @ Fri, 10 Dec 2021 10:02:38: start model_add_line... INFO @ Fri, 10 Dec 2021 10:02:38: start X-correlation... INFO @ Fri, 10 Dec 2021 10:02:38: 19000000 INFO @ Fri, 10 Dec 2021 10:02:38: end of X-cor INFO @ Fri, 10 Dec 2021 10:02:38: #2 finished! INFO @ Fri, 10 Dec 2021 10:02:38: #2 predicted fragment length is 104 bps INFO @ Fri, 10 Dec 2021 10:02:38: #2 alternative fragment length(s) may be 104 bps INFO @ Fri, 10 Dec 2021 10:02:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.05_model.r WARNING @ Fri, 10 Dec 2021 10:02:39: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:02:39: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Fri, 10 Dec 2021 10:02:39: #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 10:02:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:02:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:02:43: 24000000 INFO @ Fri, 10 Dec 2021 10:02:46: 20000000 INFO @ Fri, 10 Dec 2021 10:02:51: 25000000 INFO @ Fri, 10 Dec 2021 10:02:53: 21000000 INFO @ Fri, 10 Dec 2021 10:02:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:02:58: 26000000 INFO @ Fri, 10 Dec 2021 10:03:00: 22000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:03:06: 27000000 INFO @ Fri, 10 Dec 2021 10:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:03:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:03:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.05_summits.bed INFO @ Fri, 10 Dec 2021 10:03:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11739 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:03:08: 23000000 INFO @ Fri, 10 Dec 2021 10:03:13: 28000000 INFO @ Fri, 10 Dec 2021 10:03:15: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:03:15: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:03:15: #1 total tags in treatment: 12044493 INFO @ Fri, 10 Dec 2021 10:03:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:03:15: #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 10:03:15: 24000000 INFO @ Fri, 10 Dec 2021 10:03:15: #1 tags after filtering in treatment: 9607618 INFO @ Fri, 10 Dec 2021 10:03:15: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 10 Dec 2021 10:03:15: #1 finished! INFO @ Fri, 10 Dec 2021 10:03:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:03:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:03:16: #2 number of paired peaks: 1027 INFO @ Fri, 10 Dec 2021 10:03:16: start model_add_line... INFO @ Fri, 10 Dec 2021 10:03:16: start X-correlation... INFO @ Fri, 10 Dec 2021 10:03:16: end of X-cor INFO @ Fri, 10 Dec 2021 10:03:16: #2 finished! INFO @ Fri, 10 Dec 2021 10:03:16: #2 predicted fragment length is 104 bps INFO @ Fri, 10 Dec 2021 10:03:16: #2 alternative fragment length(s) may be 104 bps INFO @ Fri, 10 Dec 2021 10:03:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.10_model.r WARNING @ Fri, 10 Dec 2021 10:03:16: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:03:16: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Fri, 10 Dec 2021 10:03:16: #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 10:03:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:03:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:03:21: 25000000 INFO @ Fri, 10 Dec 2021 10:03:28: 26000000 INFO @ Fri, 10 Dec 2021 10:03:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:03:34: 27000000 INFO @ Fri, 10 Dec 2021 10:03:40: 28000000 INFO @ Fri, 10 Dec 2021 10:03:42: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:03:42: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:03:42: #1 total tags in treatment: 12044493 INFO @ Fri, 10 Dec 2021 10:03:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:03:42: #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 10:03:42: #1 tags after filtering in treatment: 9607618 INFO @ Fri, 10 Dec 2021 10:03:42: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 10 Dec 2021 10:03:42: #1 finished! INFO @ Fri, 10 Dec 2021 10:03:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:03:43: #2 number of paired peaks: 1027 INFO @ Fri, 10 Dec 2021 10:03:43: start model_add_line... INFO @ Fri, 10 Dec 2021 10:03:43: start X-correlation... INFO @ Fri, 10 Dec 2021 10:03:43: end of X-cor INFO @ Fri, 10 Dec 2021 10:03:43: #2 finished! INFO @ Fri, 10 Dec 2021 10:03:43: #2 predicted fragment length is 104 bps INFO @ Fri, 10 Dec 2021 10:03:43: #2 alternative fragment length(s) may be 104 bps INFO @ Fri, 10 Dec 2021 10:03:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.20_model.r WARNING @ Fri, 10 Dec 2021 10:03:43: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:03:43: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Fri, 10 Dec 2021 10:03:43: #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 10:03:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:03:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:03:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:03:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:03:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.10_summits.bed INFO @ Fri, 10 Dec 2021 10:03:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5999 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:04:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:04:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:04:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:04:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9343229/SRX9343229.20_summits.bed INFO @ Fri, 10 Dec 2021 10:04:11: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1475 records, 4 fields): 2 millis CompletedMACS2peakCalling