Job ID = 16438116 SRX = SRX14148461 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21188144 spots for SRR17992810/SRR17992810.sra Written 21188144 spots for SRR17992810/SRR17992810.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438520 ("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: 00:11:03 21188144 reads; of these: 21188144 (100.00%) were unpaired; of these: 1162305 (5.49%) aligned 0 times 10657915 (50.30%) aligned exactly 1 time 9367924 (44.21%) aligned >1 times 94.51% overall alignment rate Time searching: 00:11:04 Overall time: 00:11:04 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 12 files... [bam_rmdupse_core] 4151228 / 20025839 = 0.2073 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:58:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.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 @ Tue, 02 Aug 2022 13:58:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:58:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:58:26: 1000000 INFO @ Tue, 02 Aug 2022 13:58:32: 2000000 INFO @ Tue, 02 Aug 2022 13:58:38: 3000000 INFO @ Tue, 02 Aug 2022 13:58:44: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:58:49: 5000000 INFO @ Tue, 02 Aug 2022 13:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.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 @ Tue, 02 Aug 2022 13:58:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:58:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:58:56: 6000000 INFO @ Tue, 02 Aug 2022 13:58:56: 1000000 INFO @ Tue, 02 Aug 2022 13:59:02: 7000000 INFO @ Tue, 02 Aug 2022 13:59:03: 2000000 INFO @ Tue, 02 Aug 2022 13:59:09: 8000000 INFO @ Tue, 02 Aug 2022 13:59:09: 3000000 INFO @ Tue, 02 Aug 2022 13:59:15: 9000000 INFO @ Tue, 02 Aug 2022 13:59:16: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:59:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.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 @ Tue, 02 Aug 2022 13:59:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:59:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:59:21: 10000000 INFO @ Tue, 02 Aug 2022 13:59:22: 5000000 INFO @ Tue, 02 Aug 2022 13:59:26: 1000000 INFO @ Tue, 02 Aug 2022 13:59:28: 11000000 INFO @ Tue, 02 Aug 2022 13:59:29: 6000000 INFO @ Tue, 02 Aug 2022 13:59:33: 2000000 INFO @ Tue, 02 Aug 2022 13:59:34: 12000000 INFO @ Tue, 02 Aug 2022 13:59:35: 7000000 INFO @ Tue, 02 Aug 2022 13:59:40: 3000000 INFO @ Tue, 02 Aug 2022 13:59:41: 13000000 INFO @ Tue, 02 Aug 2022 13:59:42: 8000000 INFO @ Tue, 02 Aug 2022 13:59:46: 4000000 INFO @ Tue, 02 Aug 2022 13:59:47: 14000000 INFO @ Tue, 02 Aug 2022 13:59:48: 9000000 INFO @ Tue, 02 Aug 2022 13:59:53: 5000000 INFO @ Tue, 02 Aug 2022 13:59:53: 15000000 INFO @ Tue, 02 Aug 2022 13:59:55: 10000000 INFO @ Tue, 02 Aug 2022 13:59:59: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:59:59: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:59:59: #1 total tags in treatment: 15874611 INFO @ Tue, 02 Aug 2022 13:59:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:59:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:59:59: #1 tags after filtering in treatment: 15874611 INFO @ Tue, 02 Aug 2022 13:59:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:59:59: #1 finished! INFO @ Tue, 02 Aug 2022 13:59:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:59:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:59:59: 6000000 INFO @ Tue, 02 Aug 2022 14:00:00: #2 number of paired peaks: 1367 INFO @ Tue, 02 Aug 2022 14:00:00: start model_add_line... INFO @ Tue, 02 Aug 2022 14:00:00: start X-correlation... INFO @ Tue, 02 Aug 2022 14:00:01: end of X-cor INFO @ Tue, 02 Aug 2022 14:00:01: #2 finished! INFO @ Tue, 02 Aug 2022 14:00:01: #2 predicted fragment length is 104 bps INFO @ Tue, 02 Aug 2022 14:00:01: #2 alternative fragment length(s) may be 4,104 bps INFO @ Tue, 02 Aug 2022 14:00:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.05_model.r WARNING @ Tue, 02 Aug 2022 14:00:01: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:00:01: #2 You may need to consider one of the other alternative d(s): 4,104 WARNING @ Tue, 02 Aug 2022 14:00:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:00:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:00:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:00:01: 11000000 INFO @ Tue, 02 Aug 2022 14:00:06: 7000000 INFO @ Tue, 02 Aug 2022 14:00:07: 12000000 INFO @ Tue, 02 Aug 2022 14:00:13: 8000000 INFO @ Tue, 02 Aug 2022 14:00:14: 13000000 INFO @ Tue, 02 Aug 2022 14:00:19: 9000000 INFO @ Tue, 02 Aug 2022 14:00:20: 14000000 INFO @ Tue, 02 Aug 2022 14:00:26: 10000000 INFO @ Tue, 02 Aug 2022 14:00:27: 15000000 INFO @ Tue, 02 Aug 2022 14:00:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:00:32: 11000000 INFO @ Tue, 02 Aug 2022 14:00:32: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:00:32: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:00:32: #1 total tags in treatment: 15874611 INFO @ Tue, 02 Aug 2022 14:00:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:00:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:00:33: #1 tags after filtering in treatment: 15874611 INFO @ Tue, 02 Aug 2022 14:00:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:00:33: #1 finished! INFO @ Tue, 02 Aug 2022 14:00:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:00:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:00:34: #2 number of paired peaks: 1367 INFO @ Tue, 02 Aug 2022 14:00:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:00:34: start X-correlation... INFO @ Tue, 02 Aug 2022 14:00:34: end of X-cor INFO @ Tue, 02 Aug 2022 14:00:34: #2 finished! INFO @ Tue, 02 Aug 2022 14:00:34: #2 predicted fragment length is 104 bps INFO @ Tue, 02 Aug 2022 14:00:34: #2 alternative fragment length(s) may be 4,104 bps INFO @ Tue, 02 Aug 2022 14:00:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.10_model.r WARNING @ Tue, 02 Aug 2022 14:00:34: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:00:34: #2 You may need to consider one of the other alternative d(s): 4,104 WARNING @ Tue, 02 Aug 2022 14:00:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:00:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:00:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:00:38: 12000000 INFO @ Tue, 02 Aug 2022 14:00:44: 13000000 INFO @ Tue, 02 Aug 2022 14:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.05_summits.bed INFO @ Tue, 02 Aug 2022 14:00:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8425 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:00:50: 14000000 INFO @ Tue, 02 Aug 2022 14:00:56: 15000000 INFO @ Tue, 02 Aug 2022 14:01:02: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:01:02: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:01:02: #1 total tags in treatment: 15874611 INFO @ Tue, 02 Aug 2022 14:01:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:01:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:01:02: #1 tags after filtering in treatment: 15874611 INFO @ Tue, 02 Aug 2022 14:01:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:01:02: #1 finished! INFO @ Tue, 02 Aug 2022 14:01:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:01:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:01:03: #2 number of paired peaks: 1367 INFO @ Tue, 02 Aug 2022 14:01:03: start model_add_line... INFO @ Tue, 02 Aug 2022 14:01:03: start X-correlation... INFO @ Tue, 02 Aug 2022 14:01:03: end of X-cor INFO @ Tue, 02 Aug 2022 14:01:03: #2 finished! INFO @ Tue, 02 Aug 2022 14:01:03: #2 predicted fragment length is 104 bps INFO @ Tue, 02 Aug 2022 14:01:03: #2 alternative fragment length(s) may be 4,104 bps INFO @ Tue, 02 Aug 2022 14:01:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.20_model.r WARNING @ Tue, 02 Aug 2022 14:01:03: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:01:03: #2 You may need to consider one of the other alternative d(s): 4,104 WARNING @ Tue, 02 Aug 2022 14:01:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:01:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:01:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:01:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:01:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:01:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:01:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.10_summits.bed INFO @ Tue, 02 Aug 2022 14:01:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5046 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:01:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:01:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:01:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:01:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148461/SRX14148461.20_summits.bed INFO @ Tue, 02 Aug 2022 14:01:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2409 records, 4 fields): 31 millis CompletedMACS2peakCalling