Job ID = 14169684 SRX = ERX3978783 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23751302 spots for ERR3975808/ERR3975808.sra Written 23751302 spots for ERR3975808/ERR3975808.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170599 ("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: 01:18:00 23751302 reads; of these: 23751302 (100.00%) were paired; of these: 7370859 (31.03%) aligned concordantly 0 times 5760292 (24.25%) aligned concordantly exactly 1 time 10620151 (44.71%) aligned concordantly >1 times ---- 7370859 pairs aligned concordantly 0 times; of these: 1978873 (26.85%) aligned discordantly 1 time ---- 5391986 pairs aligned 0 times concordantly or discordantly; of these: 10783972 mates make up the pairs; of these: 5981587 (55.47%) aligned 0 times 387887 (3.60%) aligned exactly 1 time 4414498 (40.94%) aligned >1 times 87.41% overall alignment rate Time searching: 01:18:01 Overall time: 01:18:01 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] 8665728 / 18255243 = 0.4747 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 04:43:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.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 04:43:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:43:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:44:06: 1000000 INFO @ Sat, 11 Dec 2021 04:44:13: 2000000 INFO @ Sat, 11 Dec 2021 04:44:20: 3000000 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 04:44:27: 4000000 INFO @ Sat, 11 Dec 2021 04:44:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.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 04:44:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:44:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:44:35: 5000000 INFO @ Sat, 11 Dec 2021 04:44:36: 1000000 INFO @ Sat, 11 Dec 2021 04:44:43: 6000000 INFO @ Sat, 11 Dec 2021 04:44:44: 2000000 INFO @ Sat, 11 Dec 2021 04:44:51: 7000000 INFO @ Sat, 11 Dec 2021 04:44:52: 3000000 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 04:44:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.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 04:44:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:44:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:44:59: 8000000 INFO @ Sat, 11 Dec 2021 04:45:01: 4000000 INFO @ Sat, 11 Dec 2021 04:45:07: 1000000 INFO @ Sat, 11 Dec 2021 04:45:08: 9000000 INFO @ Sat, 11 Dec 2021 04:45:09: 5000000 INFO @ Sat, 11 Dec 2021 04:45:16: 2000000 INFO @ Sat, 11 Dec 2021 04:45:17: 10000000 INFO @ Sat, 11 Dec 2021 04:45:18: 6000000 INFO @ Sat, 11 Dec 2021 04:45:26: 3000000 INFO @ Sat, 11 Dec 2021 04:45:26: 11000000 INFO @ Sat, 11 Dec 2021 04:45:27: 7000000 INFO @ Sat, 11 Dec 2021 04:45:34: 4000000 INFO @ Sat, 11 Dec 2021 04:45:35: 12000000 INFO @ Sat, 11 Dec 2021 04:45:36: 8000000 INFO @ Sat, 11 Dec 2021 04:45:43: 13000000 INFO @ Sat, 11 Dec 2021 04:45:44: 5000000 INFO @ Sat, 11 Dec 2021 04:45:45: 9000000 INFO @ Sat, 11 Dec 2021 04:45:52: 14000000 INFO @ Sat, 11 Dec 2021 04:45:53: 6000000 INFO @ Sat, 11 Dec 2021 04:45:54: 10000000 INFO @ Sat, 11 Dec 2021 04:46:00: 15000000 INFO @ Sat, 11 Dec 2021 04:46:02: 7000000 INFO @ Sat, 11 Dec 2021 04:46:03: 11000000 INFO @ Sat, 11 Dec 2021 04:46:08: 16000000 INFO @ Sat, 11 Dec 2021 04:46:11: 8000000 INFO @ Sat, 11 Dec 2021 04:46:12: 12000000 INFO @ Sat, 11 Dec 2021 04:46:16: 17000000 INFO @ Sat, 11 Dec 2021 04:46:20: 13000000 INFO @ Sat, 11 Dec 2021 04:46:20: 9000000 INFO @ Sat, 11 Dec 2021 04:46:24: 18000000 INFO @ Sat, 11 Dec 2021 04:46:28: 14000000 INFO @ Sat, 11 Dec 2021 04:46:29: 10000000 INFO @ Sat, 11 Dec 2021 04:46:32: 19000000 INFO @ Sat, 11 Dec 2021 04:46:36: 15000000 INFO @ Sat, 11 Dec 2021 04:46:39: 11000000 INFO @ Sat, 11 Dec 2021 04:46:41: 20000000 INFO @ Sat, 11 Dec 2021 04:46:44: 16000000 INFO @ Sat, 11 Dec 2021 04:46:48: 12000000 INFO @ Sat, 11 Dec 2021 04:46:50: 21000000 INFO @ Sat, 11 Dec 2021 04:46:52: 17000000 INFO @ Sat, 11 Dec 2021 04:46:56: 13000000 INFO @ Sat, 11 Dec 2021 04:46:58: 22000000 INFO @ Sat, 11 Dec 2021 04:47:00: 18000000 INFO @ Sat, 11 Dec 2021 04:47:05: 14000000 INFO @ Sat, 11 Dec 2021 04:47:07: 23000000 INFO @ Sat, 11 Dec 2021 04:47:09: 19000000 INFO @ Sat, 11 Dec 2021 04:47:13: 15000000 INFO @ Sat, 11 Dec 2021 04:47:16: 24000000 INFO @ Sat, 11 Dec 2021 04:47:17: 20000000 INFO @ Sat, 11 Dec 2021 04:47:18: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 04:47:18: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 04:47:18: #1 total tags in treatment: 7892298 INFO @ Sat, 11 Dec 2021 04:47:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:47:18: #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 04:47:18: #1 tags after filtering in treatment: 5218742 INFO @ Sat, 11 Dec 2021 04:47:18: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 04:47:18: #1 finished! INFO @ Sat, 11 Dec 2021 04:47:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:47:19: #2 number of paired peaks: 4706 INFO @ Sat, 11 Dec 2021 04:47:19: start model_add_line... INFO @ Sat, 11 Dec 2021 04:47:19: start X-correlation... INFO @ Sat, 11 Dec 2021 04:47:19: end of X-cor INFO @ Sat, 11 Dec 2021 04:47:19: #2 finished! INFO @ Sat, 11 Dec 2021 04:47:19: #2 predicted fragment length is 221 bps INFO @ Sat, 11 Dec 2021 04:47:19: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 11 Dec 2021 04:47:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.05_model.r WARNING @ Sat, 11 Dec 2021 04:47:19: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:47:19: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Sat, 11 Dec 2021 04:47:19: #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 04:47:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:47:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 04:47:21: 16000000 INFO @ Sat, 11 Dec 2021 04:47:25: 21000000 INFO @ Sat, 11 Dec 2021 04:47:28: 17000000 INFO @ Sat, 11 Dec 2021 04:47:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:47:32: 22000000 INFO @ Sat, 11 Dec 2021 04:47:36: 18000000 INFO @ Sat, 11 Dec 2021 04:47:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.05_peaks.xls INFO @ Sat, 11 Dec 2021 04:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:47:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.05_summits.bed INFO @ Sat, 11 Dec 2021 04:47:40: Done! pass1 - making usageList (15 chroms): 2 millis INFO @ Sat, 11 Dec 2021 04:47:40: 23000000 pass2 - checking and writing primary data (12564 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 04:47:43: 19000000 INFO @ Sat, 11 Dec 2021 04:47:48: 24000000 INFO @ Sat, 11 Dec 2021 04:47:50: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 04:47:50: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 04:47:50: #1 total tags in treatment: 7892298 INFO @ Sat, 11 Dec 2021 04:47:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:47:50: #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 04:47:50: #1 tags after filtering in treatment: 5218742 INFO @ Sat, 11 Dec 2021 04:47:50: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 04:47:50: #1 finished! INFO @ Sat, 11 Dec 2021 04:47:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:47:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:47:50: #2 number of paired peaks: 4706 INFO @ Sat, 11 Dec 2021 04:47:50: start model_add_line... INFO @ Sat, 11 Dec 2021 04:47:51: start X-correlation... INFO @ Sat, 11 Dec 2021 04:47:51: end of X-cor INFO @ Sat, 11 Dec 2021 04:47:51: #2 finished! INFO @ Sat, 11 Dec 2021 04:47:51: #2 predicted fragment length is 221 bps INFO @ Sat, 11 Dec 2021 04:47:51: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 11 Dec 2021 04:47:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.10_model.r WARNING @ Sat, 11 Dec 2021 04:47:51: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:47:51: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Sat, 11 Dec 2021 04:47:51: #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 04:47:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:47:51: 20000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 04:47:58: 21000000 INFO @ Sat, 11 Dec 2021 04:48:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:48:05: 22000000 INFO @ Sat, 11 Dec 2021 04:48:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.10_peaks.xls INFO @ Sat, 11 Dec 2021 04:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:48:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.10_summits.bed INFO @ Sat, 11 Dec 2021 04:48:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8137 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 04:48:12: 23000000 INFO @ Sat, 11 Dec 2021 04:48:19: 24000000 INFO @ Sat, 11 Dec 2021 04:48:21: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 04:48:21: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 04:48:21: #1 total tags in treatment: 7892298 INFO @ Sat, 11 Dec 2021 04:48:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:48:21: #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 04:48:21: #1 tags after filtering in treatment: 5218742 INFO @ Sat, 11 Dec 2021 04:48:21: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 04:48:21: #1 finished! INFO @ Sat, 11 Dec 2021 04:48:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:48:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:48:22: #2 number of paired peaks: 4706 INFO @ Sat, 11 Dec 2021 04:48:22: start model_add_line... INFO @ Sat, 11 Dec 2021 04:48:22: start X-correlation... INFO @ Sat, 11 Dec 2021 04:48:22: end of X-cor INFO @ Sat, 11 Dec 2021 04:48:22: #2 finished! INFO @ Sat, 11 Dec 2021 04:48:22: #2 predicted fragment length is 221 bps INFO @ Sat, 11 Dec 2021 04:48:22: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 11 Dec 2021 04:48:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.20_model.r WARNING @ Sat, 11 Dec 2021 04:48:22: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:48:22: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Sat, 11 Dec 2021 04:48:22: #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 04:48:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:48:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:48:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:48:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.20_peaks.xls INFO @ Sat, 11 Dec 2021 04:48:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:48:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978783/ERX3978783.20_summits.bed INFO @ Sat, 11 Dec 2021 04:48:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3950 records, 4 fields): 15 millis CompletedMACS2peakCalling