Job ID = 14168184 SRX = ERX3978834 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26125176 spots for ERR3975903/ERR3975903.sra Written 26125176 spots for ERR3975903/ERR3975903.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169565 ("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: 02:23:36 26125176 reads; of these: 26125176 (100.00%) were paired; of these: 4766206 (18.24%) aligned concordantly 0 times 11573934 (44.30%) aligned concordantly exactly 1 time 9785036 (37.45%) aligned concordantly >1 times ---- 4766206 pairs aligned concordantly 0 times; of these: 436075 (9.15%) aligned discordantly 1 time ---- 4330131 pairs aligned 0 times concordantly or discordantly; of these: 8660262 mates make up the pairs; of these: 3821363 (44.13%) aligned 0 times 1474610 (17.03%) aligned exactly 1 time 3364289 (38.85%) aligned >1 times 92.69% overall alignment rate Time searching: 02:23:36 Overall time: 02:23:36 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 20 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] 7246564 / 21559545 = 0.3361 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 18:38:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.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 18:38:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:38:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:39:04: 1000000 INFO @ Fri, 10 Dec 2021 18:39:10: 2000000 INFO @ Fri, 10 Dec 2021 18:39:17: 3000000 INFO @ Fri, 10 Dec 2021 18:39:23: 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 18:39:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.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 18:39:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:39:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:39:29: 5000000 INFO @ Fri, 10 Dec 2021 18:39:33: 1000000 INFO @ Fri, 10 Dec 2021 18:39:36: 6000000 INFO @ Fri, 10 Dec 2021 18:39:39: 2000000 INFO @ Fri, 10 Dec 2021 18:39:43: 7000000 INFO @ Fri, 10 Dec 2021 18:39:44: 3000000 INFO @ Fri, 10 Dec 2021 18:39:49: 8000000 INFO @ Fri, 10 Dec 2021 18:39:50: 4000000 INFO @ Fri, 10 Dec 2021 18:39:55: 5000000 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 18:39:56: 9000000 INFO @ Fri, 10 Dec 2021 18:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.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 18:39:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:39:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:40:01: 6000000 INFO @ Fri, 10 Dec 2021 18:40:03: 10000000 INFO @ Fri, 10 Dec 2021 18:40:03: 1000000 INFO @ Fri, 10 Dec 2021 18:40:07: 7000000 INFO @ Fri, 10 Dec 2021 18:40:09: 2000000 INFO @ Fri, 10 Dec 2021 18:40:09: 11000000 INFO @ Fri, 10 Dec 2021 18:40:12: 8000000 INFO @ Fri, 10 Dec 2021 18:40:14: 3000000 INFO @ Fri, 10 Dec 2021 18:40:16: 12000000 INFO @ Fri, 10 Dec 2021 18:40:18: 9000000 INFO @ Fri, 10 Dec 2021 18:40:20: 4000000 INFO @ Fri, 10 Dec 2021 18:40:22: 13000000 INFO @ Fri, 10 Dec 2021 18:40:23: 10000000 INFO @ Fri, 10 Dec 2021 18:40:26: 5000000 INFO @ Fri, 10 Dec 2021 18:40:29: 14000000 INFO @ Fri, 10 Dec 2021 18:40:29: 11000000 INFO @ Fri, 10 Dec 2021 18:40:31: 6000000 INFO @ Fri, 10 Dec 2021 18:40:35: 12000000 INFO @ Fri, 10 Dec 2021 18:40:35: 15000000 INFO @ Fri, 10 Dec 2021 18:40:37: 7000000 INFO @ Fri, 10 Dec 2021 18:40:40: 13000000 INFO @ Fri, 10 Dec 2021 18:40:42: 16000000 INFO @ Fri, 10 Dec 2021 18:40:43: 8000000 INFO @ Fri, 10 Dec 2021 18:40:46: 14000000 INFO @ Fri, 10 Dec 2021 18:40:48: 9000000 INFO @ Fri, 10 Dec 2021 18:40:48: 17000000 INFO @ Fri, 10 Dec 2021 18:40:51: 15000000 INFO @ Fri, 10 Dec 2021 18:40:54: 10000000 INFO @ Fri, 10 Dec 2021 18:40:55: 18000000 INFO @ Fri, 10 Dec 2021 18:40:57: 16000000 INFO @ Fri, 10 Dec 2021 18:40:59: 11000000 INFO @ Fri, 10 Dec 2021 18:41:01: 19000000 INFO @ Fri, 10 Dec 2021 18:41:02: 17000000 INFO @ Fri, 10 Dec 2021 18:41:05: 12000000 INFO @ Fri, 10 Dec 2021 18:41:08: 18000000 INFO @ Fri, 10 Dec 2021 18:41:08: 20000000 INFO @ Fri, 10 Dec 2021 18:41:10: 13000000 INFO @ Fri, 10 Dec 2021 18:41:13: 19000000 INFO @ Fri, 10 Dec 2021 18:41:14: 21000000 INFO @ Fri, 10 Dec 2021 18:41:16: 14000000 INFO @ Fri, 10 Dec 2021 18:41:19: 20000000 INFO @ Fri, 10 Dec 2021 18:41:21: 22000000 INFO @ Fri, 10 Dec 2021 18:41:21: 15000000 INFO @ Fri, 10 Dec 2021 18:41:24: 21000000 INFO @ Fri, 10 Dec 2021 18:41:27: 16000000 INFO @ Fri, 10 Dec 2021 18:41:27: 23000000 INFO @ Fri, 10 Dec 2021 18:41:30: 22000000 INFO @ Fri, 10 Dec 2021 18:41:32: 17000000 INFO @ Fri, 10 Dec 2021 18:41:34: 24000000 INFO @ Fri, 10 Dec 2021 18:41:35: 23000000 INFO @ Fri, 10 Dec 2021 18:41:38: 18000000 INFO @ Fri, 10 Dec 2021 18:41:40: 25000000 INFO @ Fri, 10 Dec 2021 18:41:41: 24000000 INFO @ Fri, 10 Dec 2021 18:41:43: 19000000 INFO @ Fri, 10 Dec 2021 18:41:46: 25000000 INFO @ Fri, 10 Dec 2021 18:41:46: 26000000 INFO @ Fri, 10 Dec 2021 18:41:49: 20000000 INFO @ Fri, 10 Dec 2021 18:41:52: 26000000 INFO @ Fri, 10 Dec 2021 18:41:53: 27000000 INFO @ Fri, 10 Dec 2021 18:41:54: 21000000 INFO @ Fri, 10 Dec 2021 18:41:57: 27000000 INFO @ Fri, 10 Dec 2021 18:42:00: 22000000 INFO @ Fri, 10 Dec 2021 18:42:00: 28000000 INFO @ Fri, 10 Dec 2021 18:42:03: 28000000 INFO @ Fri, 10 Dec 2021 18:42:05: 23000000 INFO @ Fri, 10 Dec 2021 18:42:07: 29000000 INFO @ Fri, 10 Dec 2021 18:42:09: 29000000 INFO @ Fri, 10 Dec 2021 18:42:11: 24000000 INFO @ Fri, 10 Dec 2021 18:42:13: 30000000 INFO @ Fri, 10 Dec 2021 18:42:15: 30000000 INFO @ Fri, 10 Dec 2021 18:42:16: 25000000 INFO @ Fri, 10 Dec 2021 18:42:20: 31000000 INFO @ Fri, 10 Dec 2021 18:42:21: 31000000 INFO @ Fri, 10 Dec 2021 18:42:22: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:42:27: 32000000 INFO @ Fri, 10 Dec 2021 18:42:27: 27000000 INFO @ Fri, 10 Dec 2021 18:42:28: 32000000 INFO @ Fri, 10 Dec 2021 18:42:33: 28000000 INFO @ Fri, 10 Dec 2021 18:42:34: 33000000 INFO @ Fri, 10 Dec 2021 18:42:34: 33000000 INFO @ Fri, 10 Dec 2021 18:42:39: 29000000 INFO @ Fri, 10 Dec 2021 18:42:40: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:42:40: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:42:40: #1 total tags in treatment: 14175157 INFO @ Fri, 10 Dec 2021 18:42:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:42:40: #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 18:42:40: #1 tags after filtering in treatment: 12239933 INFO @ Fri, 10 Dec 2021 18:42:40: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 18:42:40: #1 finished! INFO @ Fri, 10 Dec 2021 18:42:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:42:40: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:42:40: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:42:40: #1 total tags in treatment: 14175157 INFO @ Fri, 10 Dec 2021 18:42:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:42:40: #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 18:42:40: #1 tags after filtering in treatment: 12239933 INFO @ Fri, 10 Dec 2021 18:42:40: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 18:42:40: #1 finished! INFO @ Fri, 10 Dec 2021 18:42:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:42:41: #2 number of paired peaks: 478 WARNING @ Fri, 10 Dec 2021 18:42:41: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Fri, 10 Dec 2021 18:42:41: start model_add_line... INFO @ Fri, 10 Dec 2021 18:42:41: start X-correlation... INFO @ Fri, 10 Dec 2021 18:42:41: end of X-cor INFO @ Fri, 10 Dec 2021 18:42:41: #2 finished! INFO @ Fri, 10 Dec 2021 18:42:41: #2 predicted fragment length is 118 bps INFO @ Fri, 10 Dec 2021 18:42:41: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 10 Dec 2021 18:42:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.05_model.r WARNING @ Fri, 10 Dec 2021 18:42:41: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:42:41: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Fri, 10 Dec 2021 18:42:41: #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 18:42:41: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:42:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:42:41: #2 number of paired peaks: 478 WARNING @ Fri, 10 Dec 2021 18:42:41: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Fri, 10 Dec 2021 18:42:41: start model_add_line... INFO @ Fri, 10 Dec 2021 18:42:41: start X-correlation... INFO @ Fri, 10 Dec 2021 18:42:41: end of X-cor INFO @ Fri, 10 Dec 2021 18:42:41: #2 finished! INFO @ Fri, 10 Dec 2021 18:42:41: #2 predicted fragment length is 118 bps INFO @ Fri, 10 Dec 2021 18:42:41: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 10 Dec 2021 18:42:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.10_model.r WARNING @ Fri, 10 Dec 2021 18:42:41: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:42:41: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Fri, 10 Dec 2021 18:42:41: #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 18:42:41: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:42:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:42:44: 30000000 INFO @ Fri, 10 Dec 2021 18:42:49: 31000000 INFO @ Fri, 10 Dec 2021 18:42:55: 32000000 INFO @ Fri, 10 Dec 2021 18:43:00: 33000000 INFO @ Fri, 10 Dec 2021 18:43:05: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:43:05: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:43:05: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:43:05: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:43:05: #1 total tags in treatment: 14175157 INFO @ Fri, 10 Dec 2021 18:43:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:43:05: #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 18:43:05: #1 tags after filtering in treatment: 12239933 INFO @ Fri, 10 Dec 2021 18:43:05: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 18:43:05: #1 finished! INFO @ Fri, 10 Dec 2021 18:43:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:43:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:43:06: #2 number of paired peaks: 478 WARNING @ Fri, 10 Dec 2021 18:43:06: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Fri, 10 Dec 2021 18:43:06: start model_add_line... INFO @ Fri, 10 Dec 2021 18:43:06: start X-correlation... INFO @ Fri, 10 Dec 2021 18:43:06: end of X-cor INFO @ Fri, 10 Dec 2021 18:43:06: #2 finished! INFO @ Fri, 10 Dec 2021 18:43:06: #2 predicted fragment length is 118 bps INFO @ Fri, 10 Dec 2021 18:43:06: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 10 Dec 2021 18:43:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.20_model.r WARNING @ Fri, 10 Dec 2021 18:43:06: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:43:06: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Fri, 10 Dec 2021 18:43:06: #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 18:43:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:43:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:43:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:43:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:43:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.10_summits.bed INFO @ Fri, 10 Dec 2021 18:43:16: Done! INFO @ Fri, 10 Dec 2021 18:43:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:43:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:43:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.05_summits.bed INFO @ Fri, 10 Dec 2021 18:43:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2954 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6184 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:43:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:43:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:43:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:43:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978834/ERX3978834.20_summits.bed INFO @ Fri, 10 Dec 2021 18:43:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1210 records, 4 fields): 3 millis CompletedMACS2peakCalling