Job ID = 16438932 SRX = ERX9184106 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:11:10 prefetch.2.10.7: 1) Downloading 'ERR9630953'... 2022-08-02T05:11:10 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:12:15 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:12:15 prefetch.2.10.7: 1) 'ERR9630953' was downloaded successfully 2022-08-02T05:12:15 prefetch.2.10.7: 'ERR9630953' has 0 unresolved dependencies Read 23817672 spots for ERR9630953/ERR9630953.sra Written 23817672 spots for ERR9630953/ERR9630953.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439141 ("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: 00:14:11 23817672 reads; of these: 23817672 (100.00%) were unpaired; of these: 9809608 (41.19%) aligned 0 times 6417414 (26.94%) aligned exactly 1 time 7590650 (31.87%) aligned >1 times 58.81% overall alignment rate Time searching: 00:14:11 Overall time: 00:14:11 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] 3300114 / 14008064 = 0.2356 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 14:32:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.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 14:32:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:32:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:32:52: 1000000 INFO @ Tue, 02 Aug 2022 14:33:01: 2000000 INFO @ Tue, 02 Aug 2022 14:33:10: 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 14:33:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.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 14:33:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:33:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:33:19: 4000000 INFO @ Tue, 02 Aug 2022 14:33:22: 1000000 INFO @ Tue, 02 Aug 2022 14:33:28: 5000000 INFO @ Tue, 02 Aug 2022 14:33:31: 2000000 INFO @ Tue, 02 Aug 2022 14:33:38: 6000000 INFO @ Tue, 02 Aug 2022 14:33:41: 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 14:33:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.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 14:33:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:33:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:33:47: 7000000 INFO @ Tue, 02 Aug 2022 14:33:50: 4000000 INFO @ Tue, 02 Aug 2022 14:33:52: 1000000 INFO @ Tue, 02 Aug 2022 14:33:57: 8000000 INFO @ Tue, 02 Aug 2022 14:33:59: 5000000 INFO @ Tue, 02 Aug 2022 14:34:02: 2000000 INFO @ Tue, 02 Aug 2022 14:34:07: 9000000 INFO @ Tue, 02 Aug 2022 14:34:09: 6000000 INFO @ Tue, 02 Aug 2022 14:34:11: 3000000 INFO @ Tue, 02 Aug 2022 14:34:16: 10000000 INFO @ Tue, 02 Aug 2022 14:34:18: 7000000 INFO @ Tue, 02 Aug 2022 14:34:20: 4000000 INFO @ Tue, 02 Aug 2022 14:34:23: #1 tag size is determined as 82 bps INFO @ Tue, 02 Aug 2022 14:34:23: #1 tag size = 82 INFO @ Tue, 02 Aug 2022 14:34:23: #1 total tags in treatment: 10707950 INFO @ Tue, 02 Aug 2022 14:34:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:34:23: #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 14:34:23: #1 tags after filtering in treatment: 10707950 INFO @ Tue, 02 Aug 2022 14:34:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:34:23: #1 finished! INFO @ Tue, 02 Aug 2022 14:34:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:34:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:34:24: #2 number of paired peaks: 2104 INFO @ Tue, 02 Aug 2022 14:34:24: start model_add_line... INFO @ Tue, 02 Aug 2022 14:34:24: start X-correlation... INFO @ Tue, 02 Aug 2022 14:34:24: end of X-cor INFO @ Tue, 02 Aug 2022 14:34:24: #2 finished! INFO @ Tue, 02 Aug 2022 14:34:24: #2 predicted fragment length is 88 bps INFO @ Tue, 02 Aug 2022 14:34:24: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 02 Aug 2022 14:34:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.05_model.r WARNING @ Tue, 02 Aug 2022 14:34:24: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:34:24: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 02 Aug 2022 14:34:24: #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 14:34:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:34:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:34:28: 8000000 INFO @ Tue, 02 Aug 2022 14:34:29: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:34:37: 9000000 INFO @ Tue, 02 Aug 2022 14:34:39: 6000000 INFO @ Tue, 02 Aug 2022 14:34:46: 10000000 INFO @ Tue, 02 Aug 2022 14:34:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:34:48: 7000000 INFO @ Tue, 02 Aug 2022 14:34:52: #1 tag size is determined as 82 bps INFO @ Tue, 02 Aug 2022 14:34:52: #1 tag size = 82 INFO @ Tue, 02 Aug 2022 14:34:52: #1 total tags in treatment: 10707950 INFO @ Tue, 02 Aug 2022 14:34:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:34:52: #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 14:34:53: #1 tags after filtering in treatment: 10707950 INFO @ Tue, 02 Aug 2022 14:34:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:34:53: #1 finished! INFO @ Tue, 02 Aug 2022 14:34:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:34:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:34:53: #2 number of paired peaks: 2104 INFO @ Tue, 02 Aug 2022 14:34:53: start model_add_line... INFO @ Tue, 02 Aug 2022 14:34:54: start X-correlation... INFO @ Tue, 02 Aug 2022 14:34:54: end of X-cor INFO @ Tue, 02 Aug 2022 14:34:54: #2 finished! INFO @ Tue, 02 Aug 2022 14:34:54: #2 predicted fragment length is 88 bps INFO @ Tue, 02 Aug 2022 14:34:54: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 02 Aug 2022 14:34:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.10_model.r WARNING @ Tue, 02 Aug 2022 14:34:54: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:34:54: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 02 Aug 2022 14:34:54: #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 14:34:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:34:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:34:56: 8000000 INFO @ Tue, 02 Aug 2022 14:34:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:34:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:34:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.05_summits.bed INFO @ Tue, 02 Aug 2022 14:34:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10538 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:35:04: 9000000 INFO @ Tue, 02 Aug 2022 14:35:11: 10000000 INFO @ Tue, 02 Aug 2022 14:35:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:35:17: #1 tag size is determined as 82 bps INFO @ Tue, 02 Aug 2022 14:35:17: #1 tag size = 82 INFO @ Tue, 02 Aug 2022 14:35:17: #1 total tags in treatment: 10707950 INFO @ Tue, 02 Aug 2022 14:35:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:35:17: #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 14:35:17: #1 tags after filtering in treatment: 10707950 INFO @ Tue, 02 Aug 2022 14:35:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:35:17: #1 finished! INFO @ Tue, 02 Aug 2022 14:35:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:35:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:35:18: #2 number of paired peaks: 2104 INFO @ Tue, 02 Aug 2022 14:35:18: start model_add_line... INFO @ Tue, 02 Aug 2022 14:35:18: start X-correlation... INFO @ Tue, 02 Aug 2022 14:35:18: end of X-cor INFO @ Tue, 02 Aug 2022 14:35:18: #2 finished! INFO @ Tue, 02 Aug 2022 14:35:18: #2 predicted fragment length is 88 bps INFO @ Tue, 02 Aug 2022 14:35:18: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 02 Aug 2022 14:35:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.20_model.r WARNING @ Tue, 02 Aug 2022 14:35:18: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:35:18: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 02 Aug 2022 14:35:18: #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 14:35:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:35:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:35:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:35:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:35:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.10_summits.bed INFO @ Tue, 02 Aug 2022 14:35:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7364 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:35:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:35:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:35:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:35:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9184106/ERX9184106.20_summits.bed INFO @ Tue, 02 Aug 2022 14:35:52: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (2390 records, 4 fields): 18 millis CompletedMACS2peakCalling