Job ID = 16438989 SRX = SRX15206432 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:19:39 prefetch.2.10.7: 1) Downloading 'SRR19139379'... 2022-08-02T05:19:39 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:20:16 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:20:16 prefetch.2.10.7: 1) 'SRR19139379' was downloaded successfully 2022-08-02T05:20:16 prefetch.2.10.7: 'SRR19139379' has 0 unresolved dependencies Read 15482579 spots for SRR19139379/SRR19139379.sra Written 15482579 spots for SRR19139379/SRR19139379.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439158 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:12:34 15482579 reads; of these: 15482579 (100.00%) were unpaired; of these: 479674 (3.10%) aligned 0 times 5403420 (34.90%) aligned exactly 1 time 9599485 (62.00%) aligned >1 times 96.90% overall alignment rate Time searching: 00:12:35 Overall time: 00:12:35 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 8 files... [bam_rmdupse_core] 2495805 / 15002905 = 0.1664 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 14:40:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.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 14:40:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:40:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:40:09: 1000000 INFO @ Tue, 02 Aug 2022 14:40:17: 2000000 INFO @ Tue, 02 Aug 2022 14:40:25: 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 14:40:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.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 14:40:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:40:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:40:34: 4000000 INFO @ Tue, 02 Aug 2022 14:40:38: 1000000 INFO @ Tue, 02 Aug 2022 14:40:43: 5000000 INFO @ Tue, 02 Aug 2022 14:40:47: 2000000 INFO @ Tue, 02 Aug 2022 14:40:53: 6000000 INFO @ Tue, 02 Aug 2022 14:40:56: 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 14:41:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.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 14:41:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:41:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:41:03: 7000000 INFO @ Tue, 02 Aug 2022 14:41:05: 4000000 INFO @ Tue, 02 Aug 2022 14:41:09: 1000000 INFO @ Tue, 02 Aug 2022 14:41:12: 8000000 INFO @ Tue, 02 Aug 2022 14:41:14: 5000000 INFO @ Tue, 02 Aug 2022 14:41:17: 2000000 INFO @ Tue, 02 Aug 2022 14:41:22: 9000000 INFO @ Tue, 02 Aug 2022 14:41:23: 6000000 INFO @ Tue, 02 Aug 2022 14:41:25: 3000000 INFO @ Tue, 02 Aug 2022 14:41:32: 10000000 INFO @ Tue, 02 Aug 2022 14:41:32: 7000000 INFO @ Tue, 02 Aug 2022 14:41:34: 4000000 INFO @ Tue, 02 Aug 2022 14:41:42: 8000000 INFO @ Tue, 02 Aug 2022 14:41:43: 11000000 INFO @ Tue, 02 Aug 2022 14:41:43: 5000000 INFO @ Tue, 02 Aug 2022 14:41:51: 9000000 INFO @ Tue, 02 Aug 2022 14:41:52: 6000000 INFO @ Tue, 02 Aug 2022 14:41:52: 12000000 INFO @ Tue, 02 Aug 2022 14:41:57: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:41:57: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:41:57: #1 total tags in treatment: 12507100 INFO @ Tue, 02 Aug 2022 14:41:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:41:57: #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 14:41:58: #1 tags after filtering in treatment: 12507100 INFO @ Tue, 02 Aug 2022 14:41:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:41:58: #1 finished! INFO @ Tue, 02 Aug 2022 14:41:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:41:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:41:59: #2 number of paired peaks: 3480 INFO @ Tue, 02 Aug 2022 14:41:59: start model_add_line... INFO @ Tue, 02 Aug 2022 14:41:59: start X-correlation... INFO @ Tue, 02 Aug 2022 14:41:59: end of X-cor INFO @ Tue, 02 Aug 2022 14:41:59: #2 finished! INFO @ Tue, 02 Aug 2022 14:41:59: #2 predicted fragment length is 128 bps INFO @ Tue, 02 Aug 2022 14:41:59: #2 alternative fragment length(s) may be 4,128 bps INFO @ Tue, 02 Aug 2022 14:41:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.05_model.r WARNING @ Tue, 02 Aug 2022 14:41:59: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:41:59: #2 You may need to consider one of the other alternative d(s): 4,128 WARNING @ Tue, 02 Aug 2022 14:41:59: #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 14:41:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:42:00: 10000000 INFO @ Tue, 02 Aug 2022 14:42:02: 7000000 INFO @ Tue, 02 Aug 2022 14:42:09: 11000000 INFO @ Tue, 02 Aug 2022 14:42:12: 8000000 INFO @ Tue, 02 Aug 2022 14:42:18: 12000000 INFO @ Tue, 02 Aug 2022 14:42:21: 9000000 INFO @ Tue, 02 Aug 2022 14:42:24: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:42:24: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:42:24: #1 total tags in treatment: 12507100 INFO @ Tue, 02 Aug 2022 14:42:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:42:24: #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 14:42:24: #1 tags after filtering in treatment: 12507100 INFO @ Tue, 02 Aug 2022 14:42:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:42:24: #1 finished! INFO @ Tue, 02 Aug 2022 14:42:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:42:25: #2 number of paired peaks: 3480 INFO @ Tue, 02 Aug 2022 14:42:25: start model_add_line... INFO @ Tue, 02 Aug 2022 14:42:25: start X-correlation... INFO @ Tue, 02 Aug 2022 14:42:25: end of X-cor INFO @ Tue, 02 Aug 2022 14:42:25: #2 finished! INFO @ Tue, 02 Aug 2022 14:42:25: #2 predicted fragment length is 128 bps INFO @ Tue, 02 Aug 2022 14:42:25: #2 alternative fragment length(s) may be 4,128 bps INFO @ Tue, 02 Aug 2022 14:42:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.10_model.r WARNING @ Tue, 02 Aug 2022 14:42:25: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:42:25: #2 You may need to consider one of the other alternative d(s): 4,128 WARNING @ Tue, 02 Aug 2022 14:42:25: #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 14:42:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:42:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:42:29: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:42:31: 10000000 INFO @ Tue, 02 Aug 2022 14:42:41: 11000000 INFO @ Tue, 02 Aug 2022 14:42:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.05_summits.bed INFO @ Tue, 02 Aug 2022 14:42:45: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (13602 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:42:51: 12000000 INFO @ Tue, 02 Aug 2022 14:42:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:42:55: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:42:55: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:42:55: #1 total tags in treatment: 12507100 INFO @ Tue, 02 Aug 2022 14:42:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:42:55: #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 14:42:55: #1 tags after filtering in treatment: 12507100 INFO @ Tue, 02 Aug 2022 14:42:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:42:55: #1 finished! INFO @ Tue, 02 Aug 2022 14:42:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:42:57: #2 number of paired peaks: 3480 INFO @ Tue, 02 Aug 2022 14:42:57: start model_add_line... INFO @ Tue, 02 Aug 2022 14:42:57: start X-correlation... INFO @ Tue, 02 Aug 2022 14:42:57: end of X-cor INFO @ Tue, 02 Aug 2022 14:42:57: #2 finished! INFO @ Tue, 02 Aug 2022 14:42:57: #2 predicted fragment length is 128 bps INFO @ Tue, 02 Aug 2022 14:42:57: #2 alternative fragment length(s) may be 4,128 bps INFO @ Tue, 02 Aug 2022 14:42:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.20_model.r WARNING @ Tue, 02 Aug 2022 14:42:57: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:42:57: #2 You may need to consider one of the other alternative d(s): 4,128 WARNING @ Tue, 02 Aug 2022 14:42:57: #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 14:42:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:42:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:43:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:43:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:43:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.10_summits.bed INFO @ Tue, 02 Aug 2022 14:43:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7646 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:43:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:43:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:43:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:43:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206432/SRX15206432.20_summits.bed INFO @ Tue, 02 Aug 2022 14:43:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2692 records, 4 fields): 39 millis CompletedMACS2peakCalling