Job ID = 16438959 SRX = SRX15206528 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:15:55 prefetch.2.10.7: 1) Downloading 'SRR19139264'... 2022-08-02T05:15:55 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:16:33 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:16:34 prefetch.2.10.7: 'SRR19139264' is valid 2022-08-02T05:16:34 prefetch.2.10.7: 1) 'SRR19139264' was downloaded successfully 2022-08-02T05:16:34 prefetch.2.10.7: 'SRR19139264' has 0 unresolved dependencies Read 9032801 spots for SRR19139264/SRR19139264.sra Written 9032801 spots for SRR19139264/SRR19139264.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439129 ("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: 00:07:59 9032801 reads; of these: 9032801 (100.00%) were unpaired; of these: 683061 (7.56%) aligned 0 times 7074427 (78.32%) aligned exactly 1 time 1275313 (14.12%) aligned >1 times 92.44% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 2026629 / 8349740 = 0.2427 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 14:32:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.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 14:32:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:32:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:32:16: 1000000 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 14:32:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.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 14:32:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:32:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:32:31: 2000000 INFO @ Tue, 02 Aug 2022 14:32:46: 1000000 INFO @ Tue, 02 Aug 2022 14:32:47: 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 14:32:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.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 14:32:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:32:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:33:02: 4000000 INFO @ Tue, 02 Aug 2022 14:33:02: 2000000 INFO @ Tue, 02 Aug 2022 14:33:19: 1000000 INFO @ Tue, 02 Aug 2022 14:33:19: 3000000 INFO @ Tue, 02 Aug 2022 14:33:19: 5000000 INFO @ Tue, 02 Aug 2022 14:33:36: 6000000 INFO @ Tue, 02 Aug 2022 14:33:37: 4000000 INFO @ Tue, 02 Aug 2022 14:33:38: 2000000 INFO @ Tue, 02 Aug 2022 14:33:41: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:33:41: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:33:41: #1 total tags in treatment: 6323111 INFO @ Tue, 02 Aug 2022 14:33:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:33:41: #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 14:33:41: #1 tags after filtering in treatment: 6323111 INFO @ Tue, 02 Aug 2022 14:33:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:33:41: #1 finished! INFO @ Tue, 02 Aug 2022 14:33:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:33:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:33:42: #2 number of paired peaks: 109 WARNING @ Tue, 02 Aug 2022 14:33:42: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 02 Aug 2022 14:33:42: start model_add_line... INFO @ Tue, 02 Aug 2022 14:33:42: start X-correlation... INFO @ Tue, 02 Aug 2022 14:33:42: end of X-cor INFO @ Tue, 02 Aug 2022 14:33:42: #2 finished! INFO @ Tue, 02 Aug 2022 14:33:42: #2 predicted fragment length is 154 bps INFO @ Tue, 02 Aug 2022 14:33:42: #2 alternative fragment length(s) may be 4,154 bps INFO @ Tue, 02 Aug 2022 14:33:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.05_model.r WARNING @ Tue, 02 Aug 2022 14:33:42: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:33:42: #2 You may need to consider one of the other alternative d(s): 4,154 WARNING @ Tue, 02 Aug 2022 14:33:42: #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 14:33:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:33:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:33:53: 5000000 INFO @ Tue, 02 Aug 2022 14:33:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:33:58: 3000000 INFO @ Tue, 02 Aug 2022 14:34:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:34:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:34:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.05_summits.bed INFO @ Tue, 02 Aug 2022 14:34:03: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (248 records, 4 fields): 34 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:34:09: 6000000 INFO @ Tue, 02 Aug 2022 14:34:14: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:34:14: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:34:14: #1 total tags in treatment: 6323111 INFO @ Tue, 02 Aug 2022 14:34:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:34:14: #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 14:34:14: #1 tags after filtering in treatment: 6323111 INFO @ Tue, 02 Aug 2022 14:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:34:14: #1 finished! INFO @ Tue, 02 Aug 2022 14:34:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:34:14: #2 number of paired peaks: 109 WARNING @ Tue, 02 Aug 2022 14:34:14: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 02 Aug 2022 14:34:14: start model_add_line... INFO @ Tue, 02 Aug 2022 14:34:14: start X-correlation... INFO @ Tue, 02 Aug 2022 14:34:14: end of X-cor INFO @ Tue, 02 Aug 2022 14:34:14: #2 finished! INFO @ Tue, 02 Aug 2022 14:34:14: #2 predicted fragment length is 154 bps INFO @ Tue, 02 Aug 2022 14:34:14: #2 alternative fragment length(s) may be 4,154 bps INFO @ Tue, 02 Aug 2022 14:34:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.10_model.r WARNING @ Tue, 02 Aug 2022 14:34:14: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:34:14: #2 You may need to consider one of the other alternative d(s): 4,154 WARNING @ Tue, 02 Aug 2022 14:34:14: #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 14:34:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:34:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:34:17: 4000000 INFO @ Tue, 02 Aug 2022 14:34:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:34:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:34:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:34:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.10_summits.bed INFO @ Tue, 02 Aug 2022 14:34:35: Done! pass1 - making usageList (8 chroms): 12 millis pass2 - checking and writing primary data (101 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:34:37: 5000000 INFO @ Tue, 02 Aug 2022 14:34:57: 6000000 INFO @ Tue, 02 Aug 2022 14:35:03: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:35:03: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:35:03: #1 total tags in treatment: 6323111 INFO @ Tue, 02 Aug 2022 14:35:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:35:03: #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 14:35:04: #1 tags after filtering in treatment: 6323111 INFO @ Tue, 02 Aug 2022 14:35:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:35:04: #1 finished! INFO @ Tue, 02 Aug 2022 14:35:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:35:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:35:04: #2 number of paired peaks: 109 WARNING @ Tue, 02 Aug 2022 14:35:04: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 02 Aug 2022 14:35:04: start model_add_line... INFO @ Tue, 02 Aug 2022 14:35:04: start X-correlation... INFO @ Tue, 02 Aug 2022 14:35:04: end of X-cor INFO @ Tue, 02 Aug 2022 14:35:04: #2 finished! INFO @ Tue, 02 Aug 2022 14:35:04: #2 predicted fragment length is 154 bps INFO @ Tue, 02 Aug 2022 14:35:04: #2 alternative fragment length(s) may be 4,154 bps INFO @ Tue, 02 Aug 2022 14:35:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.20_model.r WARNING @ Tue, 02 Aug 2022 14:35:04: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:35:04: #2 You may need to consider one of the other alternative d(s): 4,154 WARNING @ Tue, 02 Aug 2022 14:35:04: #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 14:35:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:35:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:35:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:35:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:35:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:35:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206528/SRX15206528.20_summits.bed INFO @ Tue, 02 Aug 2022 14:35:24: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 20 millis CompletedMACS2peakCalling