Job ID = 14170339 SRX = SRX8689109 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25444180 spots for SRR12174342/SRR12174342.sra Written 25444180 spots for SRR12174342/SRR12174342.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170766 ("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: 00:10:02 25444180 reads; of these: 25444180 (100.00%) were unpaired; of these: 593717 (2.33%) aligned 0 times 16760896 (65.87%) aligned exactly 1 time 8089567 (31.79%) aligned >1 times 97.67% overall alignment rate Time searching: 00:10:03 Overall time: 00:10:03 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 12 files... [bam_rmdupse_core] 3172172 / 24850463 = 0.1277 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:37:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.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 @ Sat, 11 Dec 2021 06:37:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:37:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:37:43: 1000000 INFO @ Sat, 11 Dec 2021 06:37:48: 2000000 INFO @ Sat, 11 Dec 2021 06:37:53: 3000000 INFO @ Sat, 11 Dec 2021 06:37:58: 4000000 INFO @ Sat, 11 Dec 2021 06:38:04: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:38:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.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 @ Sat, 11 Dec 2021 06:38:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:38:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:38:09: 6000000 INFO @ Sat, 11 Dec 2021 06:38:13: 1000000 INFO @ Sat, 11 Dec 2021 06:38:15: 7000000 INFO @ Sat, 11 Dec 2021 06:38:19: 2000000 INFO @ Sat, 11 Dec 2021 06:38:20: 8000000 INFO @ Sat, 11 Dec 2021 06:38:24: 3000000 INFO @ Sat, 11 Dec 2021 06:38:26: 9000000 INFO @ Sat, 11 Dec 2021 06:38:30: 4000000 INFO @ Sat, 11 Dec 2021 06:38:32: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:38:36: 5000000 INFO @ Sat, 11 Dec 2021 06:38:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.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 @ Sat, 11 Dec 2021 06:38:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:38:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:38:37: 11000000 INFO @ Sat, 11 Dec 2021 06:38:42: 6000000 INFO @ Sat, 11 Dec 2021 06:38:44: 12000000 INFO @ Sat, 11 Dec 2021 06:38:44: 1000000 INFO @ Sat, 11 Dec 2021 06:38:48: 7000000 INFO @ Sat, 11 Dec 2021 06:38:50: 13000000 INFO @ Sat, 11 Dec 2021 06:38:51: 2000000 INFO @ Sat, 11 Dec 2021 06:38:54: 8000000 INFO @ Sat, 11 Dec 2021 06:38:56: 14000000 INFO @ Sat, 11 Dec 2021 06:38:58: 3000000 INFO @ Sat, 11 Dec 2021 06:39:01: 9000000 INFO @ Sat, 11 Dec 2021 06:39:02: 15000000 INFO @ Sat, 11 Dec 2021 06:39:05: 4000000 INFO @ Sat, 11 Dec 2021 06:39:07: 10000000 INFO @ Sat, 11 Dec 2021 06:39:08: 16000000 INFO @ Sat, 11 Dec 2021 06:39:12: 5000000 INFO @ Sat, 11 Dec 2021 06:39:13: 11000000 INFO @ Sat, 11 Dec 2021 06:39:15: 17000000 INFO @ Sat, 11 Dec 2021 06:39:19: 12000000 INFO @ Sat, 11 Dec 2021 06:39:19: 6000000 INFO @ Sat, 11 Dec 2021 06:39:21: 18000000 INFO @ Sat, 11 Dec 2021 06:39:25: 13000000 INFO @ Sat, 11 Dec 2021 06:39:26: 7000000 INFO @ Sat, 11 Dec 2021 06:39:27: 19000000 INFO @ Sat, 11 Dec 2021 06:39:31: 14000000 INFO @ Sat, 11 Dec 2021 06:39:33: 20000000 INFO @ Sat, 11 Dec 2021 06:39:34: 8000000 INFO @ Sat, 11 Dec 2021 06:39:37: 15000000 INFO @ Sat, 11 Dec 2021 06:39:40: 21000000 INFO @ Sat, 11 Dec 2021 06:39:41: 9000000 INFO @ Sat, 11 Dec 2021 06:39:44: 16000000 INFO @ Sat, 11 Dec 2021 06:39:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:39:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:39:44: #1 total tags in treatment: 21678291 INFO @ Sat, 11 Dec 2021 06:39:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:39:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:39:44: #1 tags after filtering in treatment: 21678291 INFO @ Sat, 11 Dec 2021 06:39:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:39:44: #1 finished! INFO @ Sat, 11 Dec 2021 06:39:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:39:46: #2 number of paired peaks: 150 WARNING @ Sat, 11 Dec 2021 06:39:46: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 11 Dec 2021 06:39:46: start model_add_line... INFO @ Sat, 11 Dec 2021 06:39:46: start X-correlation... INFO @ Sat, 11 Dec 2021 06:39:46: end of X-cor INFO @ Sat, 11 Dec 2021 06:39:46: #2 finished! INFO @ Sat, 11 Dec 2021 06:39:46: #2 predicted fragment length is 39 bps INFO @ Sat, 11 Dec 2021 06:39:46: #2 alternative fragment length(s) may be 39 bps INFO @ Sat, 11 Dec 2021 06:39:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.05_model.r WARNING @ Sat, 11 Dec 2021 06:39:46: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:39:46: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Sat, 11 Dec 2021 06:39:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:39:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:39:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:39:48: 10000000 INFO @ Sat, 11 Dec 2021 06:39:50: 17000000 INFO @ Sat, 11 Dec 2021 06:39:55: 11000000 INFO @ Sat, 11 Dec 2021 06:39:56: 18000000 INFO @ Sat, 11 Dec 2021 06:40:02: 12000000 INFO @ Sat, 11 Dec 2021 06:40:02: 19000000 INFO @ Sat, 11 Dec 2021 06:40:09: 20000000 INFO @ Sat, 11 Dec 2021 06:40:09: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:40:15: 21000000 INFO @ Sat, 11 Dec 2021 06:40:16: 14000000 INFO @ Sat, 11 Dec 2021 06:40:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:40:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:40:19: #1 total tags in treatment: 21678291 INFO @ Sat, 11 Dec 2021 06:40:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:40:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:40:20: #1 tags after filtering in treatment: 21678291 INFO @ Sat, 11 Dec 2021 06:40:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:40:20: #1 finished! INFO @ Sat, 11 Dec 2021 06:40:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:40:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:40:21: #2 number of paired peaks: 150 WARNING @ Sat, 11 Dec 2021 06:40:21: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 11 Dec 2021 06:40:21: start model_add_line... INFO @ Sat, 11 Dec 2021 06:40:21: start X-correlation... INFO @ Sat, 11 Dec 2021 06:40:21: end of X-cor INFO @ Sat, 11 Dec 2021 06:40:21: #2 finished! INFO @ Sat, 11 Dec 2021 06:40:21: #2 predicted fragment length is 39 bps INFO @ Sat, 11 Dec 2021 06:40:21: #2 alternative fragment length(s) may be 39 bps INFO @ Sat, 11 Dec 2021 06:40:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.10_model.r WARNING @ Sat, 11 Dec 2021 06:40:21: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:40:21: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Sat, 11 Dec 2021 06:40:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:40:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:40:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:40:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:40:22: 15000000 INFO @ Sat, 11 Dec 2021 06:40:29: 16000000 INFO @ Sat, 11 Dec 2021 06:40:36: 17000000 INFO @ Sat, 11 Dec 2021 06:40:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:40:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:40:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.05_summits.bed INFO @ Sat, 11 Dec 2021 06:40:40: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2230 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:40:42: 18000000 INFO @ Sat, 11 Dec 2021 06:40:49: 19000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:40:55: 20000000 INFO @ Sat, 11 Dec 2021 06:40:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:41:02: 21000000 INFO @ Sat, 11 Dec 2021 06:41:06: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:41:06: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:41:06: #1 total tags in treatment: 21678291 INFO @ Sat, 11 Dec 2021 06:41:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:41:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:41:07: #1 tags after filtering in treatment: 21678291 INFO @ Sat, 11 Dec 2021 06:41:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:41:07: #1 finished! INFO @ Sat, 11 Dec 2021 06:41:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:41:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:41:08: #2 number of paired peaks: 150 WARNING @ Sat, 11 Dec 2021 06:41:08: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 11 Dec 2021 06:41:08: start model_add_line... INFO @ Sat, 11 Dec 2021 06:41:08: start X-correlation... INFO @ Sat, 11 Dec 2021 06:41:08: end of X-cor INFO @ Sat, 11 Dec 2021 06:41:08: #2 finished! INFO @ Sat, 11 Dec 2021 06:41:08: #2 predicted fragment length is 39 bps INFO @ Sat, 11 Dec 2021 06:41:08: #2 alternative fragment length(s) may be 39 bps INFO @ Sat, 11 Dec 2021 06:41:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.20_model.r WARNING @ Sat, 11 Dec 2021 06:41:08: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:41:08: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Sat, 11 Dec 2021 06:41:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:41:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:41:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:41:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:41:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:41:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.10_summits.bed INFO @ Sat, 11 Dec 2021 06:41:17: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1593 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:41:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:42:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:42:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:42:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689109/SRX8689109.20_summits.bed INFO @ Sat, 11 Dec 2021 06:42:03: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1168 records, 4 fields): 2 millis CompletedMACS2peakCalling