Job ID = 16438942 SRX = SRX13227901 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26440924 spots for SRR17038014/SRR17038014.sra Written 26440924 spots for SRR17038014/SRR17038014.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439151 ("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: 00:16:16 26440924 reads; of these: 26440924 (100.00%) were unpaired; of these: 1233140 (4.66%) aligned 0 times 18038684 (68.22%) aligned exactly 1 time 7169100 (27.11%) aligned >1 times 95.34% overall alignment rate Time searching: 00:16:16 Overall time: 00:16:16 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] 13075462 / 25207784 = 0.5187 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 14:38:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.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 14:38:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:38:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:38:39: 1000000 INFO @ Tue, 02 Aug 2022 14:38:50: 2000000 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 14:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.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 14:38:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:38:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:39:01: 3000000 INFO @ Tue, 02 Aug 2022 14:39:10: 1000000 INFO @ Tue, 02 Aug 2022 14:39:13: 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 14:39:24: 2000000 INFO @ Tue, 02 Aug 2022 14:39:24: 5000000 INFO @ Tue, 02 Aug 2022 14:39:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.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 14:39:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:39:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:39:36: 6000000 INFO @ Tue, 02 Aug 2022 14:39:39: 3000000 INFO @ Tue, 02 Aug 2022 14:39:39: 1000000 INFO @ Tue, 02 Aug 2022 14:39:48: 7000000 INFO @ Tue, 02 Aug 2022 14:39:51: 2000000 INFO @ Tue, 02 Aug 2022 14:39:53: 4000000 INFO @ Tue, 02 Aug 2022 14:40:00: 8000000 INFO @ Tue, 02 Aug 2022 14:40:04: 3000000 INFO @ Tue, 02 Aug 2022 14:40:07: 5000000 INFO @ Tue, 02 Aug 2022 14:40:12: 9000000 INFO @ Tue, 02 Aug 2022 14:40:16: 4000000 INFO @ Tue, 02 Aug 2022 14:40:21: 6000000 INFO @ Tue, 02 Aug 2022 14:40:24: 10000000 INFO @ Tue, 02 Aug 2022 14:40:29: 5000000 INFO @ Tue, 02 Aug 2022 14:40:35: 7000000 INFO @ Tue, 02 Aug 2022 14:40:36: 11000000 INFO @ Tue, 02 Aug 2022 14:40:41: 6000000 INFO @ Tue, 02 Aug 2022 14:40:47: 12000000 INFO @ Tue, 02 Aug 2022 14:40:48: 8000000 INFO @ Tue, 02 Aug 2022 14:40:49: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:40:49: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:40:49: #1 total tags in treatment: 12132322 INFO @ Tue, 02 Aug 2022 14:40:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:40:49: #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 14:40:49: #1 tags after filtering in treatment: 12132322 INFO @ Tue, 02 Aug 2022 14:40:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:40:49: #1 finished! INFO @ Tue, 02 Aug 2022 14:40:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:40:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:40:50: #2 number of paired peaks: 151 WARNING @ Tue, 02 Aug 2022 14:40:50: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Tue, 02 Aug 2022 14:40:50: start model_add_line... INFO @ Tue, 02 Aug 2022 14:40:50: start X-correlation... INFO @ Tue, 02 Aug 2022 14:40:50: end of X-cor INFO @ Tue, 02 Aug 2022 14:40:50: #2 finished! INFO @ Tue, 02 Aug 2022 14:40:50: #2 predicted fragment length is 94 bps INFO @ Tue, 02 Aug 2022 14:40:50: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 02 Aug 2022 14:40:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.05_model.r WARNING @ Tue, 02 Aug 2022 14:40:50: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:40:50: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Tue, 02 Aug 2022 14:40:50: #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 14:40:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:40:54: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:41:02: 9000000 INFO @ Tue, 02 Aug 2022 14:41:06: 8000000 INFO @ Tue, 02 Aug 2022 14:41:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:41:16: 10000000 INFO @ Tue, 02 Aug 2022 14:41:18: 9000000 INFO @ Tue, 02 Aug 2022 14:41:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:41:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:41:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.05_summits.bed INFO @ Tue, 02 Aug 2022 14:41:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7253 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:41:29: 11000000 INFO @ Tue, 02 Aug 2022 14:41:31: 10000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:41:43: 12000000 INFO @ Tue, 02 Aug 2022 14:41:43: 11000000 INFO @ Tue, 02 Aug 2022 14:41:45: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:41:45: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:41:45: #1 total tags in treatment: 12132322 INFO @ Tue, 02 Aug 2022 14:41:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:41:45: #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 14:41:45: #1 tags after filtering in treatment: 12132322 INFO @ Tue, 02 Aug 2022 14:41:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:41:45: #1 finished! INFO @ Tue, 02 Aug 2022 14:41:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:41:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:41:46: #2 number of paired peaks: 151 WARNING @ Tue, 02 Aug 2022 14:41:46: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Tue, 02 Aug 2022 14:41:46: start model_add_line... INFO @ Tue, 02 Aug 2022 14:41:46: start X-correlation... INFO @ Tue, 02 Aug 2022 14:41:46: end of X-cor INFO @ Tue, 02 Aug 2022 14:41:46: #2 finished! INFO @ Tue, 02 Aug 2022 14:41:46: #2 predicted fragment length is 94 bps INFO @ Tue, 02 Aug 2022 14:41:46: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 02 Aug 2022 14:41:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.10_model.r WARNING @ Tue, 02 Aug 2022 14:41:46: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:41:46: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Tue, 02 Aug 2022 14:41:46: #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 14:41:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:41:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:41:56: 12000000 INFO @ Tue, 02 Aug 2022 14:41:57: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:41:57: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:41:57: #1 total tags in treatment: 12132322 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 14:41:57: #1 tags after filtering in treatment: 12132322 INFO @ Tue, 02 Aug 2022 14:41:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:41:57: #1 finished! INFO @ Tue, 02 Aug 2022 14:41:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:41:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:41:58: #2 number of paired peaks: 151 WARNING @ Tue, 02 Aug 2022 14:41:58: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Tue, 02 Aug 2022 14:41:58: start model_add_line... INFO @ Tue, 02 Aug 2022 14:41:58: 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 94 bps INFO @ Tue, 02 Aug 2022 14:41:59: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 02 Aug 2022 14:41:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.20_model.r WARNING @ Tue, 02 Aug 2022 14:41:59: #2 Since the d (94) 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): 94 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 14:42:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:42:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:42:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:42:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:42:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.10_summits.bed INFO @ Tue, 02 Aug 2022 14:42:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2621 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:42:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:42:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:42:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13227901/SRX13227901.20_summits.bed INFO @ Tue, 02 Aug 2022 14:42:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (748 records, 4 fields): 20 millis CompletedMACS2peakCalling