Job ID = 16439745 SRX = SRX14894235 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T07:04:36 prefetch.2.10.7: 1) Downloading 'SRR18795786'... 2022-08-02T07:04:36 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T07:05:56 prefetch.2.10.7: HTTPS download succeed 2022-08-02T07:05:56 prefetch.2.10.7: 1) 'SRR18795786' was downloaded successfully 2022-08-02T07:05:56 prefetch.2.10.7: 'SRR18795786' has 0 unresolved dependencies Read 58927443 spots for SRR18795786/SRR18795786.sra Written 58927443 spots for SRR18795786/SRR18795786.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439880 ("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: 00:15:48 58927443 reads; of these: 58927443 (100.00%) were unpaired; of these: 3573622 (6.06%) aligned 0 times 46643906 (79.15%) aligned exactly 1 time 8709915 (14.78%) aligned >1 times 93.94% overall alignment rate Time searching: 00:15:48 Overall time: 00:15:48 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 24 files... [bam_rmdupse_core] 42007422 / 55353821 = 0.7589 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 16:32:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.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 16:32:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:32:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:32:40: 1000000 INFO @ Tue, 02 Aug 2022 16:32:48: 2000000 INFO @ Tue, 02 Aug 2022 16:32:55: 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 16:33:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.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 16:33:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:33:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:33:02: 4000000 INFO @ Tue, 02 Aug 2022 16:33:09: 1000000 INFO @ Tue, 02 Aug 2022 16:33:10: 5000000 INFO @ Tue, 02 Aug 2022 16:33:16: 2000000 INFO @ Tue, 02 Aug 2022 16:33:17: 6000000 INFO @ Tue, 02 Aug 2022 16:33:22: 3000000 INFO @ Tue, 02 Aug 2022 16:33:25: 7000000 INFO @ Tue, 02 Aug 2022 16:33:29: 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 16:33:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.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 16:33:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:33:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:33:33: 8000000 INFO @ Tue, 02 Aug 2022 16:33:36: 5000000 INFO @ Tue, 02 Aug 2022 16:33:39: 1000000 INFO @ Tue, 02 Aug 2022 16:33:40: 9000000 INFO @ Tue, 02 Aug 2022 16:33:43: 6000000 INFO @ Tue, 02 Aug 2022 16:33:46: 2000000 INFO @ Tue, 02 Aug 2022 16:33:48: 10000000 INFO @ Tue, 02 Aug 2022 16:33:50: 7000000 INFO @ Tue, 02 Aug 2022 16:33:54: 3000000 INFO @ Tue, 02 Aug 2022 16:33:56: 11000000 INFO @ Tue, 02 Aug 2022 16:33:58: 8000000 INFO @ Tue, 02 Aug 2022 16:34:01: 4000000 INFO @ Tue, 02 Aug 2022 16:34:04: 12000000 INFO @ Tue, 02 Aug 2022 16:34:05: 9000000 INFO @ Tue, 02 Aug 2022 16:34:08: 5000000 INFO @ Tue, 02 Aug 2022 16:34:11: 13000000 INFO @ Tue, 02 Aug 2022 16:34:12: 10000000 INFO @ Tue, 02 Aug 2022 16:34:14: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:34:14: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:34:14: #1 total tags in treatment: 13346399 INFO @ Tue, 02 Aug 2022 16:34:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:34:14: #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 16:34:14: #1 tags after filtering in treatment: 13346399 INFO @ Tue, 02 Aug 2022 16:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:34:14: #1 finished! INFO @ Tue, 02 Aug 2022 16:34:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:34:15: 6000000 INFO @ Tue, 02 Aug 2022 16:34:15: #2 number of paired peaks: 5038 INFO @ Tue, 02 Aug 2022 16:34:15: start model_add_line... INFO @ Tue, 02 Aug 2022 16:34:15: start X-correlation... INFO @ Tue, 02 Aug 2022 16:34:15: end of X-cor INFO @ Tue, 02 Aug 2022 16:34:15: #2 finished! INFO @ Tue, 02 Aug 2022 16:34:15: #2 predicted fragment length is 289 bps INFO @ Tue, 02 Aug 2022 16:34:15: #2 alternative fragment length(s) may be 289 bps INFO @ Tue, 02 Aug 2022 16:34:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.05_model.r INFO @ Tue, 02 Aug 2022 16:34:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:34:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:34:19: 11000000 INFO @ Tue, 02 Aug 2022 16:34:22: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:34:26: 12000000 INFO @ Tue, 02 Aug 2022 16:34:28: 8000000 INFO @ Tue, 02 Aug 2022 16:34:32: 13000000 INFO @ Tue, 02 Aug 2022 16:34:34: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:34:34: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:34:34: #1 total tags in treatment: 13346399 INFO @ Tue, 02 Aug 2022 16:34:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:34:34: #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 16:34:34: #1 tags after filtering in treatment: 13346399 INFO @ Tue, 02 Aug 2022 16:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:34:34: #1 finished! INFO @ Tue, 02 Aug 2022 16:34:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:34:35: 9000000 INFO @ Tue, 02 Aug 2022 16:34:36: #2 number of paired peaks: 5038 INFO @ Tue, 02 Aug 2022 16:34:36: start model_add_line... INFO @ Tue, 02 Aug 2022 16:34:36: start X-correlation... INFO @ Tue, 02 Aug 2022 16:34:36: end of X-cor INFO @ Tue, 02 Aug 2022 16:34:36: #2 finished! INFO @ Tue, 02 Aug 2022 16:34:36: #2 predicted fragment length is 289 bps INFO @ Tue, 02 Aug 2022 16:34:36: #2 alternative fragment length(s) may be 289 bps INFO @ Tue, 02 Aug 2022 16:34:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.10_model.r INFO @ Tue, 02 Aug 2022 16:34:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:34:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:34:40: 10000000 INFO @ Tue, 02 Aug 2022 16:34:46: 11000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:34:52: 12000000 INFO @ Tue, 02 Aug 2022 16:34:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:34:57: 13000000 INFO @ Tue, 02 Aug 2022 16:34:59: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:34:59: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:34:59: #1 total tags in treatment: 13346399 INFO @ Tue, 02 Aug 2022 16:34:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:34:59: #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 16:34:59: #1 tags after filtering in treatment: 13346399 INFO @ Tue, 02 Aug 2022 16:34:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:34:59: #1 finished! INFO @ Tue, 02 Aug 2022 16:34:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:34:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:35:00: #2 number of paired peaks: 5038 INFO @ Tue, 02 Aug 2022 16:35:00: start model_add_line... INFO @ Tue, 02 Aug 2022 16:35:01: start X-correlation... INFO @ Tue, 02 Aug 2022 16:35:01: end of X-cor INFO @ Tue, 02 Aug 2022 16:35:01: #2 finished! INFO @ Tue, 02 Aug 2022 16:35:01: #2 predicted fragment length is 289 bps INFO @ Tue, 02 Aug 2022 16:35:01: #2 alternative fragment length(s) may be 289 bps INFO @ Tue, 02 Aug 2022 16:35:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.20_model.r INFO @ Tue, 02 Aug 2022 16:35:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:35:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:35:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:35:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:35:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.05_summits.bed INFO @ Tue, 02 Aug 2022 16:35:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11004 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:35:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:35:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:35:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:35:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.10_summits.bed INFO @ Tue, 02 Aug 2022 16:35:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9143 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:35:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:35:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:35:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:35:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894235/SRX14894235.20_summits.bed INFO @ Tue, 02 Aug 2022 16:35:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7095 records, 4 fields): 24 millis CompletedMACS2peakCalling