Job ID = 14172040 SRX = SRX9103804 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25026283 spots for SRR12621004/SRR12621004.sra Written 25026283 spots for SRR12621004/SRR12621004.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172541 ("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: 00:21:02 25026283 reads; of these: 25026283 (100.00%) were paired; of these: 8368097 (33.44%) aligned concordantly 0 times 9350461 (37.36%) aligned concordantly exactly 1 time 7307725 (29.20%) aligned concordantly >1 times ---- 8368097 pairs aligned concordantly 0 times; of these: 1455724 (17.40%) aligned discordantly 1 time ---- 6912373 pairs aligned 0 times concordantly or discordantly; of these: 13824746 mates make up the pairs; of these: 12050839 (87.17%) aligned 0 times 529621 (3.83%) aligned exactly 1 time 1244286 (9.00%) aligned >1 times 75.92% overall alignment rate Time searching: 00:21:02 Overall time: 00:21:02 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] 5562391 / 17919467 = 0.3104 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 14:21:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.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 14:21:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:21:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:21:56: 1000000 INFO @ Sat, 11 Dec 2021 14:22:01: 2000000 INFO @ Sat, 11 Dec 2021 14:22:06: 3000000 INFO @ Sat, 11 Dec 2021 14:22:11: 4000000 INFO @ Sat, 11 Dec 2021 14:22:16: 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 14:22:21: 6000000 INFO @ Sat, 11 Dec 2021 14:22:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.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 14:22:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:22:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:22:26: 7000000 INFO @ Sat, 11 Dec 2021 14:22:28: 1000000 INFO @ Sat, 11 Dec 2021 14:22:32: 8000000 INFO @ Sat, 11 Dec 2021 14:22:34: 2000000 INFO @ Sat, 11 Dec 2021 14:22:38: 9000000 INFO @ Sat, 11 Dec 2021 14:22:41: 3000000 INFO @ Sat, 11 Dec 2021 14:22:44: 10000000 INFO @ Sat, 11 Dec 2021 14:22:47: 4000000 INFO @ Sat, 11 Dec 2021 14:22:49: 11000000 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 14:22:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.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 14:22:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:22:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:22:53: 5000000 INFO @ Sat, 11 Dec 2021 14:22:55: 12000000 INFO @ Sat, 11 Dec 2021 14:22:58: 1000000 INFO @ Sat, 11 Dec 2021 14:23:00: 6000000 INFO @ Sat, 11 Dec 2021 14:23:01: 13000000 INFO @ Sat, 11 Dec 2021 14:23:05: 2000000 INFO @ Sat, 11 Dec 2021 14:23:06: 7000000 INFO @ Sat, 11 Dec 2021 14:23:07: 14000000 INFO @ Sat, 11 Dec 2021 14:23:12: 3000000 INFO @ Sat, 11 Dec 2021 14:23:12: 15000000 INFO @ Sat, 11 Dec 2021 14:23:13: 8000000 INFO @ Sat, 11 Dec 2021 14:23:18: 16000000 INFO @ Sat, 11 Dec 2021 14:23:18: 4000000 INFO @ Sat, 11 Dec 2021 14:23:19: 9000000 INFO @ Sat, 11 Dec 2021 14:23:24: 17000000 INFO @ Sat, 11 Dec 2021 14:23:25: 5000000 INFO @ Sat, 11 Dec 2021 14:23:25: 10000000 INFO @ Sat, 11 Dec 2021 14:23:30: 18000000 INFO @ Sat, 11 Dec 2021 14:23:31: 6000000 INFO @ Sat, 11 Dec 2021 14:23:32: 11000000 INFO @ Sat, 11 Dec 2021 14:23:35: 19000000 INFO @ Sat, 11 Dec 2021 14:23:38: 7000000 INFO @ Sat, 11 Dec 2021 14:23:38: 12000000 INFO @ Sat, 11 Dec 2021 14:23:41: 20000000 INFO @ Sat, 11 Dec 2021 14:23:44: 8000000 INFO @ Sat, 11 Dec 2021 14:23:45: 13000000 INFO @ Sat, 11 Dec 2021 14:23:46: 21000000 INFO @ Sat, 11 Dec 2021 14:23:51: 9000000 INFO @ Sat, 11 Dec 2021 14:23:51: 14000000 INFO @ Sat, 11 Dec 2021 14:23:52: 22000000 INFO @ Sat, 11 Dec 2021 14:23:57: 10000000 INFO @ Sat, 11 Dec 2021 14:23:57: 15000000 INFO @ Sat, 11 Dec 2021 14:23:58: 23000000 INFO @ Sat, 11 Dec 2021 14:24:04: 11000000 INFO @ Sat, 11 Dec 2021 14:24:04: 16000000 INFO @ Sat, 11 Dec 2021 14:24:04: 24000000 INFO @ Sat, 11 Dec 2021 14:24:10: 25000000 INFO @ Sat, 11 Dec 2021 14:24:10: 17000000 INFO @ Sat, 11 Dec 2021 14:24:10: 12000000 INFO @ Sat, 11 Dec 2021 14:24:15: 26000000 INFO @ Sat, 11 Dec 2021 14:24:16: 18000000 INFO @ Sat, 11 Dec 2021 14:24:17: 13000000 INFO @ Sat, 11 Dec 2021 14:24:21: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:24:21: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:24:21: #1 total tags in treatment: 11214659 INFO @ Sat, 11 Dec 2021 14:24:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:24:21: #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 14:24:21: #1 tags after filtering in treatment: 8541164 INFO @ Sat, 11 Dec 2021 14:24:21: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 14:24:21: #1 finished! INFO @ Sat, 11 Dec 2021 14:24:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:24:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:24:21: #2 number of paired peaks: 1281 INFO @ Sat, 11 Dec 2021 14:24:21: start model_add_line... INFO @ Sat, 11 Dec 2021 14:24:21: start X-correlation... INFO @ Sat, 11 Dec 2021 14:24:21: end of X-cor INFO @ Sat, 11 Dec 2021 14:24:21: #2 finished! INFO @ Sat, 11 Dec 2021 14:24:21: #2 predicted fragment length is 76 bps INFO @ Sat, 11 Dec 2021 14:24:21: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 11 Dec 2021 14:24:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.05_model.r WARNING @ Sat, 11 Dec 2021 14:24:21: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:24:21: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 11 Dec 2021 14:24:21: #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 14:24:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:24:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:24:23: 19000000 INFO @ Sat, 11 Dec 2021 14:24:23: 14000000 INFO @ Sat, 11 Dec 2021 14:24:29: 20000000 INFO @ Sat, 11 Dec 2021 14:24:30: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:24:35: 21000000 INFO @ Sat, 11 Dec 2021 14:24:36: 16000000 INFO @ Sat, 11 Dec 2021 14:24:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:24:42: 22000000 INFO @ Sat, 11 Dec 2021 14:24:43: 17000000 INFO @ Sat, 11 Dec 2021 14:24:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:24:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:24:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.05_summits.bed INFO @ Sat, 11 Dec 2021 14:24:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9834 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:24:48: 23000000 INFO @ Sat, 11 Dec 2021 14:24:49: 18000000 INFO @ Sat, 11 Dec 2021 14:24:54: 24000000 INFO @ Sat, 11 Dec 2021 14:24:56: 19000000 INFO @ Sat, 11 Dec 2021 14:25:00: 25000000 INFO @ Sat, 11 Dec 2021 14:25:02: 20000000 INFO @ Sat, 11 Dec 2021 14:25:07: 26000000 INFO @ Sat, 11 Dec 2021 14:25:08: 21000000 INFO @ Sat, 11 Dec 2021 14:25:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:25:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:25:12: #1 total tags in treatment: 11214659 INFO @ Sat, 11 Dec 2021 14:25:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:25:12: #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 14:25:12: #1 tags after filtering in treatment: 8541164 INFO @ Sat, 11 Dec 2021 14:25:12: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 14:25:12: #1 finished! INFO @ Sat, 11 Dec 2021 14:25:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:25:13: #2 number of paired peaks: 1281 INFO @ Sat, 11 Dec 2021 14:25:13: start model_add_line... INFO @ Sat, 11 Dec 2021 14:25:13: start X-correlation... INFO @ Sat, 11 Dec 2021 14:25:13: end of X-cor INFO @ Sat, 11 Dec 2021 14:25:13: #2 finished! INFO @ Sat, 11 Dec 2021 14:25:13: #2 predicted fragment length is 76 bps INFO @ Sat, 11 Dec 2021 14:25:13: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 11 Dec 2021 14:25:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.10_model.r WARNING @ Sat, 11 Dec 2021 14:25:13: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:25:13: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 11 Dec 2021 14:25:13: #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 14:25:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:25:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:25:15: 22000000 INFO @ Sat, 11 Dec 2021 14:25:21: 23000000 INFO @ Sat, 11 Dec 2021 14:25:27: 24000000 INFO @ Sat, 11 Dec 2021 14:25:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:25:33: 25000000 INFO @ Sat, 11 Dec 2021 14:25:39: 26000000 INFO @ Sat, 11 Dec 2021 14:25:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:25:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:25:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.10_summits.bed INFO @ Sat, 11 Dec 2021 14:25:39: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4953 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:25:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:25:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:25:44: #1 total tags in treatment: 11214659 INFO @ Sat, 11 Dec 2021 14:25:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:25:44: #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 14:25:44: #1 tags after filtering in treatment: 8541164 INFO @ Sat, 11 Dec 2021 14:25:44: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 14:25:44: #1 finished! INFO @ Sat, 11 Dec 2021 14:25:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:25:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:25:45: #2 number of paired peaks: 1281 INFO @ Sat, 11 Dec 2021 14:25:45: start model_add_line... INFO @ Sat, 11 Dec 2021 14:25:45: start X-correlation... INFO @ Sat, 11 Dec 2021 14:25:45: end of X-cor INFO @ Sat, 11 Dec 2021 14:25:45: #2 finished! INFO @ Sat, 11 Dec 2021 14:25:45: #2 predicted fragment length is 76 bps INFO @ Sat, 11 Dec 2021 14:25:45: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 11 Dec 2021 14:25:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.20_model.r WARNING @ Sat, 11 Dec 2021 14:25:45: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:25:45: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 11 Dec 2021 14:25:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:25:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:25:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:26:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:26:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:26:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:26:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103804/SRX9103804.20_summits.bed INFO @ Sat, 11 Dec 2021 14:26:11: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (972 records, 4 fields): 3 millis CompletedMACS2peakCalling