Job ID = 14168384 SRX = ERX3978745 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29757882 spots for ERR3975755/ERR3975755.sra Written 29757882 spots for ERR3975755/ERR3975755.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169693 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:58:44 29757882 reads; of these: 29757882 (100.00%) were paired; of these: 11266604 (37.86%) aligned concordantly 0 times 10025190 (33.69%) aligned concordantly exactly 1 time 8466088 (28.45%) aligned concordantly >1 times ---- 11266604 pairs aligned concordantly 0 times; of these: 2855846 (25.35%) aligned discordantly 1 time ---- 8410758 pairs aligned 0 times concordantly or discordantly; of these: 16821516 mates make up the pairs; of these: 10446918 (62.10%) aligned 0 times 633156 (3.76%) aligned exactly 1 time 5741442 (34.13%) aligned >1 times 82.45% overall alignment rate Time searching: 00:58:45 Overall time: 00:58:45 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 36 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 7502262 / 21199594 = 0.3539 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 @ Fri, 10 Dec 2021 19:35:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.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 @ Fri, 10 Dec 2021 19:35:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:35:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:35:51: 1000000 INFO @ Fri, 10 Dec 2021 19:35:57: 2000000 INFO @ Fri, 10 Dec 2021 19:36:03: 3000000 INFO @ Fri, 10 Dec 2021 19:36:09: 4000000 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 @ Fri, 10 Dec 2021 19:36:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.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 @ Fri, 10 Dec 2021 19:36:14: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:36:14: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:36:15: 5000000 INFO @ Fri, 10 Dec 2021 19:36:21: 1000000 INFO @ Fri, 10 Dec 2021 19:36:22: 6000000 INFO @ Fri, 10 Dec 2021 19:36:27: 2000000 INFO @ Fri, 10 Dec 2021 19:36:29: 7000000 INFO @ Fri, 10 Dec 2021 19:36:34: 3000000 INFO @ Fri, 10 Dec 2021 19:36:35: 8000000 INFO @ Fri, 10 Dec 2021 19:36:41: 4000000 INFO @ Fri, 10 Dec 2021 19:36:42: 9000000 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 @ Fri, 10 Dec 2021 19:36:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.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 @ Fri, 10 Dec 2021 19:36:44: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:36:44: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:36:48: 5000000 INFO @ Fri, 10 Dec 2021 19:36:49: 10000000 INFO @ Fri, 10 Dec 2021 19:36:52: 1000000 INFO @ Fri, 10 Dec 2021 19:36:55: 6000000 INFO @ Fri, 10 Dec 2021 19:36:56: 11000000 INFO @ Fri, 10 Dec 2021 19:37:00: 2000000 INFO @ Fri, 10 Dec 2021 19:37:02: 7000000 INFO @ Fri, 10 Dec 2021 19:37:03: 12000000 INFO @ Fri, 10 Dec 2021 19:37:08: 3000000 INFO @ Fri, 10 Dec 2021 19:37:09: 8000000 INFO @ Fri, 10 Dec 2021 19:37:10: 13000000 INFO @ Fri, 10 Dec 2021 19:37:16: 4000000 INFO @ Fri, 10 Dec 2021 19:37:16: 9000000 INFO @ Fri, 10 Dec 2021 19:37:17: 14000000 INFO @ Fri, 10 Dec 2021 19:37:23: 10000000 INFO @ Fri, 10 Dec 2021 19:37:23: 5000000 INFO @ Fri, 10 Dec 2021 19:37:24: 15000000 INFO @ Fri, 10 Dec 2021 19:37:30: 11000000 INFO @ Fri, 10 Dec 2021 19:37:31: 16000000 INFO @ Fri, 10 Dec 2021 19:37:31: 6000000 INFO @ Fri, 10 Dec 2021 19:37:37: 12000000 INFO @ Fri, 10 Dec 2021 19:37:38: 17000000 INFO @ Fri, 10 Dec 2021 19:37:39: 7000000 INFO @ Fri, 10 Dec 2021 19:37:45: 13000000 INFO @ Fri, 10 Dec 2021 19:37:45: 18000000 INFO @ Fri, 10 Dec 2021 19:37:47: 8000000 INFO @ Fri, 10 Dec 2021 19:37:52: 14000000 INFO @ Fri, 10 Dec 2021 19:37:52: 19000000 INFO @ Fri, 10 Dec 2021 19:37:55: 9000000 INFO @ Fri, 10 Dec 2021 19:37:59: 15000000 INFO @ Fri, 10 Dec 2021 19:37:59: 20000000 INFO @ Fri, 10 Dec 2021 19:38:03: 10000000 INFO @ Fri, 10 Dec 2021 19:38:06: 16000000 INFO @ Fri, 10 Dec 2021 19:38:06: 21000000 INFO @ Fri, 10 Dec 2021 19:38:11: 11000000 INFO @ Fri, 10 Dec 2021 19:38:12: 22000000 INFO @ Fri, 10 Dec 2021 19:38:13: 17000000 INFO @ Fri, 10 Dec 2021 19:38:19: 12000000 INFO @ Fri, 10 Dec 2021 19:38:19: 23000000 INFO @ Fri, 10 Dec 2021 19:38:20: 18000000 INFO @ Fri, 10 Dec 2021 19:38:25: 24000000 INFO @ Fri, 10 Dec 2021 19:38:26: 13000000 INFO @ Fri, 10 Dec 2021 19:38:26: 19000000 INFO @ Fri, 10 Dec 2021 19:38:32: 25000000 INFO @ Fri, 10 Dec 2021 19:38:33: 20000000 INFO @ Fri, 10 Dec 2021 19:38:34: 14000000 INFO @ Fri, 10 Dec 2021 19:38:38: 26000000 INFO @ Fri, 10 Dec 2021 19:38:40: 21000000 INFO @ Fri, 10 Dec 2021 19:38:42: 15000000 INFO @ Fri, 10 Dec 2021 19:38:45: 27000000 INFO @ Fri, 10 Dec 2021 19:38:46: 22000000 INFO @ Fri, 10 Dec 2021 19:38:50: 16000000 INFO @ Fri, 10 Dec 2021 19:38:52: 28000000 INFO @ Fri, 10 Dec 2021 19:38:53: 23000000 INFO @ Fri, 10 Dec 2021 19:38:58: 17000000 INFO @ Fri, 10 Dec 2021 19:38:59: 29000000 INFO @ Fri, 10 Dec 2021 19:38:59: 24000000 INFO @ Fri, 10 Dec 2021 19:39:05: 30000000 INFO @ Fri, 10 Dec 2021 19:39:06: 18000000 INFO @ Fri, 10 Dec 2021 19:39:06: 25000000 INFO @ Fri, 10 Dec 2021 19:39:12: 26000000 INFO @ Fri, 10 Dec 2021 19:39:12: 31000000 INFO @ Fri, 10 Dec 2021 19:39:13: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:39:19: 27000000 INFO @ Fri, 10 Dec 2021 19:39:19: 32000000 INFO @ Fri, 10 Dec 2021 19:39:21: 20000000 INFO @ Fri, 10 Dec 2021 19:39:25: 28000000 INFO @ Fri, 10 Dec 2021 19:39:26: 33000000 INFO @ Fri, 10 Dec 2021 19:39:29: 21000000 INFO @ Fri, 10 Dec 2021 19:39:32: 29000000 INFO @ Fri, 10 Dec 2021 19:39:33: 34000000 INFO @ Fri, 10 Dec 2021 19:39:33: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:39:33: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:39:33: #1 total tags in treatment: 11305350 INFO @ Fri, 10 Dec 2021 19:39:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:39:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 19:39:34: #1 tags after filtering in treatment: 8010289 INFO @ Fri, 10 Dec 2021 19:39:34: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 19:39:34: #1 finished! INFO @ Fri, 10 Dec 2021 19:39:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:39:34: #2 number of paired peaks: 3842 INFO @ Fri, 10 Dec 2021 19:39:34: start model_add_line... INFO @ Fri, 10 Dec 2021 19:39:34: start X-correlation... INFO @ Fri, 10 Dec 2021 19:39:35: end of X-cor INFO @ Fri, 10 Dec 2021 19:39:35: #2 finished! INFO @ Fri, 10 Dec 2021 19:39:35: #2 predicted fragment length is 201 bps INFO @ Fri, 10 Dec 2021 19:39:35: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 10 Dec 2021 19:39:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.05_model.r WARNING @ Fri, 10 Dec 2021 19:39:35: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:39:35: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Fri, 10 Dec 2021 19:39:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 19:39:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:39:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:39:36: 22000000 INFO @ Fri, 10 Dec 2021 19:39:39: 30000000 INFO @ Fri, 10 Dec 2021 19:39:43: 23000000 INFO @ Fri, 10 Dec 2021 19:39:46: 31000000 INFO @ Fri, 10 Dec 2021 19:39:51: 24000000 INFO @ Fri, 10 Dec 2021 19:39:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:39:53: 32000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:39:58: 25000000 INFO @ Fri, 10 Dec 2021 19:40:00: 33000000 INFO @ Fri, 10 Dec 2021 19:40:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:40:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:40:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.05_summits.bed INFO @ Fri, 10 Dec 2021 19:40:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11569 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:40:06: 26000000 INFO @ Fri, 10 Dec 2021 19:40:06: 34000000 INFO @ Fri, 10 Dec 2021 19:40:07: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:40:07: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:40:07: #1 total tags in treatment: 11305350 INFO @ Fri, 10 Dec 2021 19:40:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:40:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 19:40:07: #1 tags after filtering in treatment: 8010289 INFO @ Fri, 10 Dec 2021 19:40:07: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 19:40:07: #1 finished! INFO @ Fri, 10 Dec 2021 19:40:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:40:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:40:08: #2 number of paired peaks: 3842 INFO @ Fri, 10 Dec 2021 19:40:08: start model_add_line... INFO @ Fri, 10 Dec 2021 19:40:08: start X-correlation... INFO @ Fri, 10 Dec 2021 19:40:08: end of X-cor INFO @ Fri, 10 Dec 2021 19:40:08: #2 finished! INFO @ Fri, 10 Dec 2021 19:40:08: #2 predicted fragment length is 201 bps INFO @ Fri, 10 Dec 2021 19:40:08: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 10 Dec 2021 19:40:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.10_model.r WARNING @ Fri, 10 Dec 2021 19:40:08: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:40:08: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Fri, 10 Dec 2021 19:40:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 19:40:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:40:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:40:13: 27000000 INFO @ Fri, 10 Dec 2021 19:40:20: 28000000 INFO @ Fri, 10 Dec 2021 19:40:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:40:28: 29000000 INFO @ Fri, 10 Dec 2021 19:40:35: 30000000 INFO @ Fri, 10 Dec 2021 19:40:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:40:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:40:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.10_summits.bed INFO @ Fri, 10 Dec 2021 19:40:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7720 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:40:43: 31000000 INFO @ Fri, 10 Dec 2021 19:40:50: 32000000 INFO @ Fri, 10 Dec 2021 19:40:58: 33000000 INFO @ Fri, 10 Dec 2021 19:41:05: 34000000 INFO @ Fri, 10 Dec 2021 19:41:06: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:41:06: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:41:06: #1 total tags in treatment: 11305350 INFO @ Fri, 10 Dec 2021 19:41:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:41:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 19:41:06: #1 tags after filtering in treatment: 8010289 INFO @ Fri, 10 Dec 2021 19:41:06: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 19:41:06: #1 finished! INFO @ Fri, 10 Dec 2021 19:41:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:41:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:41:07: #2 number of paired peaks: 3842 INFO @ Fri, 10 Dec 2021 19:41:07: start model_add_line... INFO @ Fri, 10 Dec 2021 19:41:07: start X-correlation... INFO @ Fri, 10 Dec 2021 19:41:07: end of X-cor INFO @ Fri, 10 Dec 2021 19:41:07: #2 finished! INFO @ Fri, 10 Dec 2021 19:41:07: #2 predicted fragment length is 201 bps INFO @ Fri, 10 Dec 2021 19:41:07: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 10 Dec 2021 19:41:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.20_model.r WARNING @ Fri, 10 Dec 2021 19:41:07: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:41:07: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Fri, 10 Dec 2021 19:41:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 19:41:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:41:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:41:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:41:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:41:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:41:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978745/ERX3978745.20_summits.bed INFO @ Fri, 10 Dec 2021 19:41:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3465 records, 4 fields): 13 millis CompletedMACS2peakCalling