Job ID = 16439195 SRX = SRX15206472 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:46:45 prefetch.2.10.7: 1) Downloading 'SRR19139334'... 2022-08-02T05:46:46 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:47:01 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:47:02 prefetch.2.10.7: 'SRR19139334' is valid 2022-08-02T05:47:02 prefetch.2.10.7: 1) 'SRR19139334' was downloaded successfully 2022-08-02T05:47:02 prefetch.2.10.7: 'SRR19139334' has 0 unresolved dependencies Read 8241442 spots for SRR19139334/SRR19139334.sra Written 8241442 spots for SRR19139334/SRR19139334.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439326 ("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: 00:04:40 8241442 reads; of these: 8241442 (100.00%) were unpaired; of these: 171024 (2.08%) aligned 0 times 3506697 (42.55%) aligned exactly 1 time 4563721 (55.38%) aligned >1 times 97.92% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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_rmdupse_core] 1836752 / 8070418 = 0.2276 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 14:55:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.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 14:55:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:55:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:55:39: 1000000 INFO @ Tue, 02 Aug 2022 14:55:46: 2000000 INFO @ Tue, 02 Aug 2022 14:55:54: 3000000 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 14:56:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.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 14:56:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:56:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:56:02: 4000000 INFO @ Tue, 02 Aug 2022 14:56:09: 1000000 INFO @ Tue, 02 Aug 2022 14:56:09: 5000000 INFO @ Tue, 02 Aug 2022 14:56:17: 6000000 INFO @ Tue, 02 Aug 2022 14:56:17: 2000000 INFO @ Tue, 02 Aug 2022 14:56:18: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:56:18: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:56:18: #1 total tags in treatment: 6233666 INFO @ Tue, 02 Aug 2022 14:56:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:56:18: #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 14:56:19: #1 tags after filtering in treatment: 6233666 INFO @ Tue, 02 Aug 2022 14:56:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:56:19: #1 finished! INFO @ Tue, 02 Aug 2022 14:56:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:56:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:56:20: #2 number of paired peaks: 5042 INFO @ Tue, 02 Aug 2022 14:56:20: start model_add_line... INFO @ Tue, 02 Aug 2022 14:56:20: start X-correlation... INFO @ Tue, 02 Aug 2022 14:56:20: end of X-cor INFO @ Tue, 02 Aug 2022 14:56:20: #2 finished! INFO @ Tue, 02 Aug 2022 14:56:20: #2 predicted fragment length is 143 bps INFO @ Tue, 02 Aug 2022 14:56:20: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 02 Aug 2022 14:56:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.05_model.r WARNING @ Tue, 02 Aug 2022 14:56:20: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:56:20: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 02 Aug 2022 14:56:20: #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 14:56:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:56:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:56:26: 3000000 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 14:56:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.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 14:56:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:56:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:56:34: 4000000 INFO @ Tue, 02 Aug 2022 14:56:38: 1000000 INFO @ Tue, 02 Aug 2022 14:56:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:56:43: 5000000 INFO @ Tue, 02 Aug 2022 14:56:46: 2000000 INFO @ Tue, 02 Aug 2022 14:56:51: 6000000 INFO @ Tue, 02 Aug 2022 14:56:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:56:53: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:56:53: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:56:53: #1 total tags in treatment: 6233666 INFO @ Tue, 02 Aug 2022 14:56:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:56:53: #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 14:56:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:56:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.05_summits.bed INFO @ Tue, 02 Aug 2022 14:56:54: #1 tags after filtering in treatment: 6233666 INFO @ Tue, 02 Aug 2022 14:56:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:56:54: #1 finished! INFO @ Tue, 02 Aug 2022 14:56:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:56:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:56:54: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8918 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:56:54: 3000000 INFO @ Tue, 02 Aug 2022 14:56:55: #2 number of paired peaks: 5042 INFO @ Tue, 02 Aug 2022 14:56:55: start model_add_line... INFO @ Tue, 02 Aug 2022 14:56:55: start X-correlation... INFO @ Tue, 02 Aug 2022 14:56:55: end of X-cor INFO @ Tue, 02 Aug 2022 14:56:55: #2 finished! INFO @ Tue, 02 Aug 2022 14:56:55: #2 predicted fragment length is 143 bps INFO @ Tue, 02 Aug 2022 14:56:55: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 02 Aug 2022 14:56:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.10_model.r WARNING @ Tue, 02 Aug 2022 14:56:55: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:56:55: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 02 Aug 2022 14:56:55: #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 14:56:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:56:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:57:02: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:57:10: 5000000 INFO @ Tue, 02 Aug 2022 14:57:18: 6000000 INFO @ Tue, 02 Aug 2022 14:57:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:57:20: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:57:20: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:57:20: #1 total tags in treatment: 6233666 INFO @ Tue, 02 Aug 2022 14:57:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:57:20: #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 14:57:20: #1 tags after filtering in treatment: 6233666 INFO @ Tue, 02 Aug 2022 14:57:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:57:20: #1 finished! INFO @ Tue, 02 Aug 2022 14:57:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:57:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:57:21: #2 number of paired peaks: 5042 INFO @ Tue, 02 Aug 2022 14:57:21: start model_add_line... INFO @ Tue, 02 Aug 2022 14:57:21: start X-correlation... INFO @ Tue, 02 Aug 2022 14:57:21: end of X-cor INFO @ Tue, 02 Aug 2022 14:57:21: #2 finished! INFO @ Tue, 02 Aug 2022 14:57:21: #2 predicted fragment length is 143 bps INFO @ Tue, 02 Aug 2022 14:57:21: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 02 Aug 2022 14:57:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.20_model.r WARNING @ Tue, 02 Aug 2022 14:57:21: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:57:21: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 02 Aug 2022 14:57:21: #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 14:57:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:57:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:57:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:57:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:57:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.10_summits.bed INFO @ Tue, 02 Aug 2022 14:57:29: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6121 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:57:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206472/SRX15206472.20_summits.bed INFO @ Tue, 02 Aug 2022 14:57:54: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3150 records, 4 fields): 129 millis CompletedMACS2peakCalling