Job ID = 14168819 SRX = ERX3978778 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17890253 spots for ERR3975799/ERR3975799.sra Written 17890253 spots for ERR3975799/ERR3975799.sra Read 27357583 spots for ERR3975801/ERR3975801.sra Written 27357583 spots for ERR3975801/ERR3975801.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170018 ("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: 01:43:04 45247836 reads; of these: 45247836 (100.00%) were paired; of these: 16558558 (36.60%) aligned concordantly 0 times 4220561 (9.33%) aligned concordantly exactly 1 time 24468717 (54.08%) aligned concordantly >1 times ---- 16558558 pairs aligned concordantly 0 times; of these: 1504731 (9.09%) aligned discordantly 1 time ---- 15053827 pairs aligned 0 times concordantly or discordantly; of these: 30107654 mates make up the pairs; of these: 14225412 (47.25%) aligned 0 times 530594 (1.76%) aligned exactly 1 time 15351648 (50.99%) aligned >1 times 84.28% overall alignment rate Time searching: 01:43:04 Overall time: 01:43:04 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 56 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] 22083885 / 29882983 = 0.7390 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 22:51:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.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 22:51:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:51:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:51:15: 1000000 INFO @ Fri, 10 Dec 2021 22:51:22: 2000000 INFO @ Fri, 10 Dec 2021 22:51:29: 3000000 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 22:51:36: 4000000 INFO @ Fri, 10 Dec 2021 22:51:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.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 22:51:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:51:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:51:44: 5000000 INFO @ Fri, 10 Dec 2021 22:51:44: 1000000 INFO @ Fri, 10 Dec 2021 22:51:52: 6000000 INFO @ Fri, 10 Dec 2021 22:51:52: 2000000 INFO @ Fri, 10 Dec 2021 22:51:59: 3000000 INFO @ Fri, 10 Dec 2021 22:52:00: 7000000 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 22:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.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 22:52:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:52:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:52:07: 8000000 INFO @ Fri, 10 Dec 2021 22:52:07: 4000000 INFO @ Fri, 10 Dec 2021 22:52:15: 9000000 INFO @ Fri, 10 Dec 2021 22:52:16: 1000000 INFO @ Fri, 10 Dec 2021 22:52:17: 5000000 INFO @ Fri, 10 Dec 2021 22:52:23: 10000000 INFO @ Fri, 10 Dec 2021 22:52:24: 2000000 INFO @ Fri, 10 Dec 2021 22:52:26: 6000000 INFO @ Fri, 10 Dec 2021 22:52:30: 11000000 INFO @ Fri, 10 Dec 2021 22:52:34: 3000000 INFO @ Fri, 10 Dec 2021 22:52:35: 7000000 INFO @ Fri, 10 Dec 2021 22:52:37: 12000000 INFO @ Fri, 10 Dec 2021 22:52:43: 4000000 INFO @ Fri, 10 Dec 2021 22:52:44: 13000000 INFO @ Fri, 10 Dec 2021 22:52:44: 8000000 INFO @ Fri, 10 Dec 2021 22:52:51: 14000000 INFO @ Fri, 10 Dec 2021 22:52:52: 9000000 INFO @ Fri, 10 Dec 2021 22:52:52: 5000000 INFO @ Fri, 10 Dec 2021 22:52:58: 15000000 INFO @ Fri, 10 Dec 2021 22:53:00: 10000000 INFO @ Fri, 10 Dec 2021 22:53:01: 6000000 INFO @ Fri, 10 Dec 2021 22:53:05: 16000000 INFO @ Fri, 10 Dec 2021 22:53:08: 11000000 INFO @ Fri, 10 Dec 2021 22:53:10: 7000000 INFO @ Fri, 10 Dec 2021 22:53:12: 17000000 INFO @ Fri, 10 Dec 2021 22:53:16: 12000000 INFO @ Fri, 10 Dec 2021 22:53:19: 18000000 INFO @ Fri, 10 Dec 2021 22:53:19: 8000000 INFO @ Fri, 10 Dec 2021 22:53:23: 13000000 INFO @ Fri, 10 Dec 2021 22:53:26: 19000000 INFO @ Fri, 10 Dec 2021 22:53:28: 9000000 INFO @ Fri, 10 Dec 2021 22:53:31: 14000000 INFO @ Fri, 10 Dec 2021 22:53:33: 20000000 INFO @ Fri, 10 Dec 2021 22:53:36: 10000000 INFO @ Fri, 10 Dec 2021 22:53:39: 15000000 INFO @ Fri, 10 Dec 2021 22:53:40: 21000000 INFO @ Fri, 10 Dec 2021 22:53:44: 11000000 INFO @ Fri, 10 Dec 2021 22:53:47: 16000000 INFO @ Fri, 10 Dec 2021 22:53:47: 22000000 INFO @ Fri, 10 Dec 2021 22:53:52: 12000000 INFO @ Fri, 10 Dec 2021 22:53:54: 23000000 INFO @ Fri, 10 Dec 2021 22:53:55: 17000000 INFO @ Fri, 10 Dec 2021 22:54:00: 13000000 INFO @ Fri, 10 Dec 2021 22:54:01: 24000000 INFO @ Fri, 10 Dec 2021 22:54:02: 18000000 INFO @ Fri, 10 Dec 2021 22:54:07: 25000000 INFO @ Fri, 10 Dec 2021 22:54:07: 14000000 INFO @ Fri, 10 Dec 2021 22:54:10: 19000000 INFO @ Fri, 10 Dec 2021 22:54:14: 26000000 INFO @ Fri, 10 Dec 2021 22:54:16: 15000000 INFO @ Fri, 10 Dec 2021 22:54:18: 20000000 INFO @ Fri, 10 Dec 2021 22:54:20: 27000000 INFO @ Fri, 10 Dec 2021 22:54:24: 16000000 INFO @ Fri, 10 Dec 2021 22:54:27: 28000000 INFO @ Fri, 10 Dec 2021 22:54:27: 21000000 INFO @ Fri, 10 Dec 2021 22:54:32: 17000000 INFO @ Fri, 10 Dec 2021 22:54:34: 29000000 INFO @ Fri, 10 Dec 2021 22:54:35: 22000000 INFO @ Fri, 10 Dec 2021 22:54:40: 18000000 INFO @ Fri, 10 Dec 2021 22:54:41: 30000000 INFO @ Fri, 10 Dec 2021 22:54:43: 23000000 INFO @ Fri, 10 Dec 2021 22:54:47: 19000000 INFO @ Fri, 10 Dec 2021 22:54:49: 31000000 INFO @ Fri, 10 Dec 2021 22:54:51: 24000000 INFO @ Fri, 10 Dec 2021 22:54:55: 20000000 INFO @ Fri, 10 Dec 2021 22:54:57: 32000000 INFO @ Fri, 10 Dec 2021 22:54:58: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 22:54:58: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 22:54:58: #1 total tags in treatment: 6803040 INFO @ Fri, 10 Dec 2021 22:54:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:54:58: #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 22:54:58: #1 tags after filtering in treatment: 4276545 INFO @ Fri, 10 Dec 2021 22:54:58: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 10 Dec 2021 22:54:58: #1 finished! INFO @ Fri, 10 Dec 2021 22:54:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:54:59: #2 number of paired peaks: 2866 INFO @ Fri, 10 Dec 2021 22:54:59: start model_add_line... INFO @ Fri, 10 Dec 2021 22:54:59: start X-correlation... INFO @ Fri, 10 Dec 2021 22:54:59: end of X-cor INFO @ Fri, 10 Dec 2021 22:54:59: #2 finished! INFO @ Fri, 10 Dec 2021 22:54:59: #2 predicted fragment length is 205 bps INFO @ Fri, 10 Dec 2021 22:54:59: #2 alternative fragment length(s) may be 205 bps INFO @ Fri, 10 Dec 2021 22:54:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.05_model.r WARNING @ Fri, 10 Dec 2021 22:54:59: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:54:59: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Fri, 10 Dec 2021 22:54:59: #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 22:54:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:54:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:55:00: 25000000 INFO @ Fri, 10 Dec 2021 22:55:03: 21000000 INFO @ Fri, 10 Dec 2021 22:55:08: 26000000 INFO @ Fri, 10 Dec 2021 22:55:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:55:11: 22000000 INFO @ Fri, 10 Dec 2021 22:55:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.05_peaks.xls INFO @ Fri, 10 Dec 2021 22:55:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:55:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.05_summits.bed INFO @ Fri, 10 Dec 2021 22:55:16: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6537 records, 4 fields): 10 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:55:17: 27000000 INFO @ Fri, 10 Dec 2021 22:55:19: 23000000 INFO @ Fri, 10 Dec 2021 22:55:24: 28000000 INFO @ Fri, 10 Dec 2021 22:55:26: 24000000 INFO @ Fri, 10 Dec 2021 22:55:32: 29000000 INFO @ Fri, 10 Dec 2021 22:55:34: 25000000 INFO @ Fri, 10 Dec 2021 22:55:41: 26000000 INFO @ Fri, 10 Dec 2021 22:55:41: 30000000 INFO @ Fri, 10 Dec 2021 22:55:47: 27000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 22:55:51: 31000000 INFO @ Fri, 10 Dec 2021 22:55:54: 28000000 INFO @ Fri, 10 Dec 2021 22:55:59: 32000000 INFO @ Fri, 10 Dec 2021 22:56:00: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 22:56:00: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 22:56:00: #1 total tags in treatment: 6803040 INFO @ Fri, 10 Dec 2021 22:56:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:56:00: #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 22:56:00: #1 tags after filtering in treatment: 4276545 INFO @ Fri, 10 Dec 2021 22:56:00: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 10 Dec 2021 22:56:00: #1 finished! INFO @ Fri, 10 Dec 2021 22:56:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:56:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:56:01: #2 number of paired peaks: 2866 INFO @ Fri, 10 Dec 2021 22:56:01: start model_add_line... INFO @ Fri, 10 Dec 2021 22:56:01: start X-correlation... INFO @ Fri, 10 Dec 2021 22:56:01: end of X-cor INFO @ Fri, 10 Dec 2021 22:56:01: #2 finished! INFO @ Fri, 10 Dec 2021 22:56:01: #2 predicted fragment length is 205 bps INFO @ Fri, 10 Dec 2021 22:56:01: #2 alternative fragment length(s) may be 205 bps INFO @ Fri, 10 Dec 2021 22:56:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.10_model.r WARNING @ Fri, 10 Dec 2021 22:56:01: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:56:01: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Fri, 10 Dec 2021 22:56:01: #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 22:56:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:56:03: 29000000 INFO @ Fri, 10 Dec 2021 22:56:11: 30000000 INFO @ Fri, 10 Dec 2021 22:56:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.10_peaks.xls INFO @ Fri, 10 Dec 2021 22:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.10_summits.bed INFO @ Fri, 10 Dec 2021 22:56:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3269 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:56:20: 31000000 INFO @ Fri, 10 Dec 2021 22:56:28: 32000000 INFO @ Fri, 10 Dec 2021 22:56:29: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 22:56:29: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 22:56:29: #1 total tags in treatment: 6803040 INFO @ Fri, 10 Dec 2021 22:56:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:56:29: #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 22:56:29: #1 tags after filtering in treatment: 4276545 INFO @ Fri, 10 Dec 2021 22:56:29: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 10 Dec 2021 22:56:29: #1 finished! INFO @ Fri, 10 Dec 2021 22:56:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:56:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:56:29: #2 number of paired peaks: 2866 INFO @ Fri, 10 Dec 2021 22:56:29: start model_add_line... INFO @ Fri, 10 Dec 2021 22:56:29: start X-correlation... INFO @ Fri, 10 Dec 2021 22:56:29: end of X-cor INFO @ Fri, 10 Dec 2021 22:56:29: #2 finished! INFO @ Fri, 10 Dec 2021 22:56:29: #2 predicted fragment length is 205 bps INFO @ Fri, 10 Dec 2021 22:56:29: #2 alternative fragment length(s) may be 205 bps INFO @ Fri, 10 Dec 2021 22:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.20_model.r WARNING @ Fri, 10 Dec 2021 22:56:29: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:56:29: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Fri, 10 Dec 2021 22:56:29: #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 22:56:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:56:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:56:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.20_peaks.xls INFO @ Fri, 10 Dec 2021 22:56:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:56:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978778/ERX3978778.20_summits.bed INFO @ Fri, 10 Dec 2021 22:56:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (935 records, 4 fields): 3 millis CompletedMACS2peakCalling