Job ID = 14171364 SRX = SRX9304583 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34611832 spots for SRR12837080/SRR12837080.sra Written 34611832 spots for SRR12837080/SRR12837080.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172068 ("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: 00:51:27 34611832 reads; of these: 34611832 (100.00%) were paired; of these: 7014828 (20.27%) aligned concordantly 0 times 22428631 (64.80%) aligned concordantly exactly 1 time 5168373 (14.93%) aligned concordantly >1 times ---- 7014828 pairs aligned concordantly 0 times; of these: 347606 (4.96%) aligned discordantly 1 time ---- 6667222 pairs aligned 0 times concordantly or discordantly; of these: 13334444 mates make up the pairs; of these: 12472288 (93.53%) aligned 0 times 559625 (4.20%) aligned exactly 1 time 302531 (2.27%) aligned >1 times 81.98% overall alignment rate Time searching: 00:51:27 Overall time: 00:51:27 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 24 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] 14128123 / 20311442 = 0.6956 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 12:32:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.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 12:32:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:32:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:32:25: 1000000 INFO @ Sat, 11 Dec 2021 12:32:31: 2000000 INFO @ Sat, 11 Dec 2021 12:32:37: 3000000 INFO @ Sat, 11 Dec 2021 12:32:43: 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 @ Sat, 11 Dec 2021 12:32:49: 5000000 INFO @ Sat, 11 Dec 2021 12:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.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 12:32:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:32:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:32:55: 6000000 INFO @ Sat, 11 Dec 2021 12:32:55: 1000000 INFO @ Sat, 11 Dec 2021 12:33:00: 2000000 INFO @ Sat, 11 Dec 2021 12:33:01: 7000000 INFO @ Sat, 11 Dec 2021 12:33:06: 3000000 INFO @ Sat, 11 Dec 2021 12:33:07: 8000000 INFO @ Sat, 11 Dec 2021 12:33:11: 4000000 INFO @ Sat, 11 Dec 2021 12:33:13: 9000000 INFO @ Sat, 11 Dec 2021 12:33:16: 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 12:33:19: 10000000 INFO @ Sat, 11 Dec 2021 12:33:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.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 12:33:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:33:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:33:21: 6000000 INFO @ Sat, 11 Dec 2021 12:33:25: 1000000 INFO @ Sat, 11 Dec 2021 12:33:25: 11000000 INFO @ Sat, 11 Dec 2021 12:33:27: 7000000 INFO @ Sat, 11 Dec 2021 12:33:31: 2000000 INFO @ Sat, 11 Dec 2021 12:33:31: 12000000 INFO @ Sat, 11 Dec 2021 12:33:32: 8000000 INFO @ Sat, 11 Dec 2021 12:33:36: 3000000 INFO @ Sat, 11 Dec 2021 12:33:37: 13000000 INFO @ Sat, 11 Dec 2021 12:33:38: 9000000 INFO @ Sat, 11 Dec 2021 12:33:42: 4000000 INFO @ Sat, 11 Dec 2021 12:33:43: 14000000 INFO @ Sat, 11 Dec 2021 12:33:44: 10000000 INFO @ Sat, 11 Dec 2021 12:33:47: 5000000 INFO @ Sat, 11 Dec 2021 12:33:49: 11000000 INFO @ Sat, 11 Dec 2021 12:33:49: 15000000 INFO @ Sat, 11 Dec 2021 12:33:53: 6000000 INFO @ Sat, 11 Dec 2021 12:33:54: 12000000 INFO @ Sat, 11 Dec 2021 12:33:55: 16000000 INFO @ Sat, 11 Dec 2021 12:33:58: 7000000 INFO @ Sat, 11 Dec 2021 12:34:00: 13000000 INFO @ Sat, 11 Dec 2021 12:34:01: 17000000 INFO @ Sat, 11 Dec 2021 12:34:03: 8000000 INFO @ Sat, 11 Dec 2021 12:34:05: 14000000 INFO @ Sat, 11 Dec 2021 12:34:07: 18000000 INFO @ Sat, 11 Dec 2021 12:34:09: 9000000 INFO @ Sat, 11 Dec 2021 12:34:11: 15000000 INFO @ Sat, 11 Dec 2021 12:34:14: 19000000 INFO @ Sat, 11 Dec 2021 12:34:14: 10000000 INFO @ Sat, 11 Dec 2021 12:34:16: 16000000 INFO @ Sat, 11 Dec 2021 12:34:20: 11000000 INFO @ Sat, 11 Dec 2021 12:34:20: 20000000 INFO @ Sat, 11 Dec 2021 12:34:22: 17000000 INFO @ Sat, 11 Dec 2021 12:34:25: 12000000 INFO @ Sat, 11 Dec 2021 12:34:26: 21000000 INFO @ Sat, 11 Dec 2021 12:34:27: 18000000 INFO @ Sat, 11 Dec 2021 12:34:30: 13000000 INFO @ Sat, 11 Dec 2021 12:34:32: 19000000 INFO @ Sat, 11 Dec 2021 12:34:33: 22000000 INFO @ Sat, 11 Dec 2021 12:34:36: 14000000 INFO @ Sat, 11 Dec 2021 12:34:38: 20000000 INFO @ Sat, 11 Dec 2021 12:34:39: 23000000 INFO @ Sat, 11 Dec 2021 12:34:41: 15000000 INFO @ Sat, 11 Dec 2021 12:34:43: 21000000 INFO @ Sat, 11 Dec 2021 12:34:46: 24000000 INFO @ Sat, 11 Dec 2021 12:34:46: 16000000 INFO @ Sat, 11 Dec 2021 12:34:49: 22000000 INFO @ Sat, 11 Dec 2021 12:34:52: 17000000 INFO @ Sat, 11 Dec 2021 12:34:52: 25000000 INFO @ Sat, 11 Dec 2021 12:34:55: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:34:58: 18000000 INFO @ Sat, 11 Dec 2021 12:34:59: 26000000 INFO @ Sat, 11 Dec 2021 12:35:01: 24000000 INFO @ Sat, 11 Dec 2021 12:35:03: 19000000 INFO @ Sat, 11 Dec 2021 12:35:05: 27000000 INFO @ Sat, 11 Dec 2021 12:35:07: 25000000 INFO @ Sat, 11 Dec 2021 12:35:09: 20000000 INFO @ Sat, 11 Dec 2021 12:35:11: 28000000 INFO @ Sat, 11 Dec 2021 12:35:13: 26000000 INFO @ Sat, 11 Dec 2021 12:35:14: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 12:35:14: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 12:35:14: #1 total tags in treatment: 13543085 INFO @ Sat, 11 Dec 2021 12:35:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:35:14: #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 12:35:14: 21000000 INFO @ Sat, 11 Dec 2021 12:35:15: #1 tags after filtering in treatment: 6009141 INFO @ Sat, 11 Dec 2021 12:35:15: #1 Redundant rate of treatment: 0.56 INFO @ Sat, 11 Dec 2021 12:35:15: #1 finished! INFO @ Sat, 11 Dec 2021 12:35:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:35:15: #2 number of paired peaks: 4960 INFO @ Sat, 11 Dec 2021 12:35:15: start model_add_line... INFO @ Sat, 11 Dec 2021 12:35:15: start X-correlation... INFO @ Sat, 11 Dec 2021 12:35:15: end of X-cor INFO @ Sat, 11 Dec 2021 12:35:15: #2 finished! INFO @ Sat, 11 Dec 2021 12:35:15: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 12:35:15: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 12:35:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.05_model.r WARNING @ Sat, 11 Dec 2021 12:35:15: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:35:15: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 12:35:15: #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 12:35:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:35:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:35:19: 27000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:35:20: 22000000 INFO @ Sat, 11 Dec 2021 12:35:24: 28000000 INFO @ Sat, 11 Dec 2021 12:35:26: 23000000 INFO @ Sat, 11 Dec 2021 12:35:27: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 12:35:27: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 12:35:27: #1 total tags in treatment: 13543085 INFO @ Sat, 11 Dec 2021 12:35:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:35:27: #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 12:35:27: #1 tags after filtering in treatment: 6009141 INFO @ Sat, 11 Dec 2021 12:35:27: #1 Redundant rate of treatment: 0.56 INFO @ Sat, 11 Dec 2021 12:35:27: #1 finished! INFO @ Sat, 11 Dec 2021 12:35:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:35:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:35:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:35:28: #2 number of paired peaks: 4960 INFO @ Sat, 11 Dec 2021 12:35:28: start model_add_line... INFO @ Sat, 11 Dec 2021 12:35:28: start X-correlation... INFO @ Sat, 11 Dec 2021 12:35:28: end of X-cor INFO @ Sat, 11 Dec 2021 12:35:28: #2 finished! INFO @ Sat, 11 Dec 2021 12:35:28: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 12:35:28: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 12:35:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.10_model.r WARNING @ Sat, 11 Dec 2021 12:35:28: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:35:28: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 12:35:28: #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 12:35:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:35:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:35:32: 24000000 INFO @ Sat, 11 Dec 2021 12:35:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:35:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:35:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.05_summits.bed INFO @ Sat, 11 Dec 2021 12:35:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (14446 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:35:37: 25000000 INFO @ Sat, 11 Dec 2021 12:35:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:35:42: 26000000 INFO @ Sat, 11 Dec 2021 12:35:47: 27000000 INFO @ Sat, 11 Dec 2021 12:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.10_summits.bed INFO @ Sat, 11 Dec 2021 12:35:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9560 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:35:52: 28000000 INFO @ Sat, 11 Dec 2021 12:35:54: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 12:35:54: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 12:35:54: #1 total tags in treatment: 13543085 INFO @ Sat, 11 Dec 2021 12:35:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:35:54: #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 12:35:55: #1 tags after filtering in treatment: 6009141 INFO @ Sat, 11 Dec 2021 12:35:55: #1 Redundant rate of treatment: 0.56 INFO @ Sat, 11 Dec 2021 12:35:55: #1 finished! INFO @ Sat, 11 Dec 2021 12:35:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:35:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:35:55: #2 number of paired peaks: 4960 INFO @ Sat, 11 Dec 2021 12:35:55: start model_add_line... INFO @ Sat, 11 Dec 2021 12:35:55: start X-correlation... INFO @ Sat, 11 Dec 2021 12:35:56: end of X-cor INFO @ Sat, 11 Dec 2021 12:35:56: #2 finished! INFO @ Sat, 11 Dec 2021 12:35:56: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 12:35:56: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 12:35:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.20_model.r WARNING @ Sat, 11 Dec 2021 12:35:56: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:35:56: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 12:35:56: #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 12:35:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:35:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:36:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:36:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:36:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304583/SRX9304583.20_summits.bed INFO @ Sat, 11 Dec 2021 12:36:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4239 records, 4 fields): 5 millis CompletedMACS2peakCalling