Job ID = 14159554 SRX = SRX8845648 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25233363 spots for SRR12345955/SRR12345955.sra Written 25233363 spots for SRR12345955/SRR12345955.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159948 ("srTce11") 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: 00:30:09 25233363 reads; of these: 25233363 (100.00%) were paired; of these: 10336690 (40.96%) aligned concordantly 0 times 13014037 (51.57%) aligned concordantly exactly 1 time 1882636 (7.46%) aligned concordantly >1 times ---- 10336690 pairs aligned concordantly 0 times; of these: 2296784 (22.22%) aligned discordantly 1 time ---- 8039906 pairs aligned 0 times concordantly or discordantly; of these: 16079812 mates make up the pairs; of these: 15011448 (93.36%) aligned 0 times 349805 (2.18%) aligned exactly 1 time 718559 (4.47%) aligned >1 times 70.25% overall alignment rate Time searching: 00:30:09 Overall time: 00:30:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 24 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 4258218 / 17112511 = 0.2488 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 @ Wed, 08 Dec 2021 23:13:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 23:13:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:13:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:13:15: 1000000 INFO @ Wed, 08 Dec 2021 23:13:22: 2000000 INFO @ Wed, 08 Dec 2021 23:13:28: 3000000 INFO @ Wed, 08 Dec 2021 23:13:35: 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 @ Wed, 08 Dec 2021 23:13:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 23:13:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:13:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:13:42: 5000000 INFO @ Wed, 08 Dec 2021 23:13:46: 1000000 INFO @ Wed, 08 Dec 2021 23:13:49: 6000000 INFO @ Wed, 08 Dec 2021 23:13:53: 2000000 INFO @ Wed, 08 Dec 2021 23:13:56: 7000000 INFO @ Wed, 08 Dec 2021 23:14:00: 3000000 INFO @ Wed, 08 Dec 2021 23:14:03: 8000000 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 @ Wed, 08 Dec 2021 23:14:07: 4000000 INFO @ Wed, 08 Dec 2021 23:14:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 23:14:08: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:14:08: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:14:11: 9000000 INFO @ Wed, 08 Dec 2021 23:14:15: 5000000 INFO @ Wed, 08 Dec 2021 23:14:16: 1000000 INFO @ Wed, 08 Dec 2021 23:14:18: 10000000 INFO @ Wed, 08 Dec 2021 23:14:22: 6000000 INFO @ Wed, 08 Dec 2021 23:14:23: 2000000 INFO @ Wed, 08 Dec 2021 23:14:25: 11000000 INFO @ Wed, 08 Dec 2021 23:14:29: 7000000 INFO @ Wed, 08 Dec 2021 23:14:30: 3000000 INFO @ Wed, 08 Dec 2021 23:14:33: 12000000 INFO @ Wed, 08 Dec 2021 23:14:37: 8000000 INFO @ Wed, 08 Dec 2021 23:14:37: 4000000 INFO @ Wed, 08 Dec 2021 23:14:40: 13000000 INFO @ Wed, 08 Dec 2021 23:14:44: 9000000 INFO @ Wed, 08 Dec 2021 23:14:44: 5000000 INFO @ Wed, 08 Dec 2021 23:14:47: 14000000 INFO @ Wed, 08 Dec 2021 23:14:52: 6000000 INFO @ Wed, 08 Dec 2021 23:14:52: 10000000 INFO @ Wed, 08 Dec 2021 23:14:54: 15000000 INFO @ Wed, 08 Dec 2021 23:14:59: 7000000 INFO @ Wed, 08 Dec 2021 23:14:59: 11000000 INFO @ Wed, 08 Dec 2021 23:15:02: 16000000 INFO @ Wed, 08 Dec 2021 23:15:06: 8000000 INFO @ Wed, 08 Dec 2021 23:15:06: 12000000 INFO @ Wed, 08 Dec 2021 23:15:09: 17000000 INFO @ Wed, 08 Dec 2021 23:15:14: 9000000 INFO @ Wed, 08 Dec 2021 23:15:14: 13000000 INFO @ Wed, 08 Dec 2021 23:15:16: 18000000 INFO @ Wed, 08 Dec 2021 23:15:21: 10000000 INFO @ Wed, 08 Dec 2021 23:15:21: 14000000 INFO @ Wed, 08 Dec 2021 23:15:23: 19000000 INFO @ Wed, 08 Dec 2021 23:15:28: 11000000 INFO @ Wed, 08 Dec 2021 23:15:28: 15000000 INFO @ Wed, 08 Dec 2021 23:15:30: 20000000 INFO @ Wed, 08 Dec 2021 23:15:35: 12000000 INFO @ Wed, 08 Dec 2021 23:15:35: 16000000 INFO @ Wed, 08 Dec 2021 23:15:37: 21000000 INFO @ Wed, 08 Dec 2021 23:15:42: 13000000 INFO @ Wed, 08 Dec 2021 23:15:42: 17000000 INFO @ Wed, 08 Dec 2021 23:15:45: 22000000 INFO @ Wed, 08 Dec 2021 23:15:49: 14000000 INFO @ Wed, 08 Dec 2021 23:15:50: 18000000 INFO @ Wed, 08 Dec 2021 23:15:52: 23000000 INFO @ Wed, 08 Dec 2021 23:15:56: 15000000 INFO @ Wed, 08 Dec 2021 23:15:57: 19000000 INFO @ Wed, 08 Dec 2021 23:16:00: 24000000 INFO @ Wed, 08 Dec 2021 23:16:03: 16000000 INFO @ Wed, 08 Dec 2021 23:16:04: 20000000 INFO @ Wed, 08 Dec 2021 23:16:07: 25000000 INFO @ Wed, 08 Dec 2021 23:16:11: 17000000 INFO @ Wed, 08 Dec 2021 23:16:11: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:16:15: 26000000 INFO @ Wed, 08 Dec 2021 23:16:18: 18000000 INFO @ Wed, 08 Dec 2021 23:16:18: 22000000 INFO @ Wed, 08 Dec 2021 23:16:22: #1 tag size is determined as 125 bps INFO @ Wed, 08 Dec 2021 23:16:22: #1 tag size = 125 INFO @ Wed, 08 Dec 2021 23:16:22: #1 total tags in treatment: 11214676 INFO @ Wed, 08 Dec 2021 23:16:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:16:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:16:22: #1 tags after filtering in treatment: 8190678 INFO @ Wed, 08 Dec 2021 23:16:22: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 08 Dec 2021 23:16:22: #1 finished! INFO @ Wed, 08 Dec 2021 23:16:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:16:23: #2 number of paired peaks: 733 WARNING @ Wed, 08 Dec 2021 23:16:23: Fewer paired peaks (733) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 733 pairs to build model! INFO @ Wed, 08 Dec 2021 23:16:23: start model_add_line... INFO @ Wed, 08 Dec 2021 23:16:23: start X-correlation... INFO @ Wed, 08 Dec 2021 23:16:23: end of X-cor INFO @ Wed, 08 Dec 2021 23:16:23: #2 finished! INFO @ Wed, 08 Dec 2021 23:16:23: #2 predicted fragment length is 210 bps INFO @ Wed, 08 Dec 2021 23:16:23: #2 alternative fragment length(s) may be 210 bps INFO @ Wed, 08 Dec 2021 23:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.05_model.r WARNING @ Wed, 08 Dec 2021 23:16:23: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:16:23: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Wed, 08 Dec 2021 23:16:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:16:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:16:26: 19000000 INFO @ Wed, 08 Dec 2021 23:16:26: 23000000 INFO @ Wed, 08 Dec 2021 23:16:33: 20000000 INFO @ Wed, 08 Dec 2021 23:16:34: 24000000 INFO @ Wed, 08 Dec 2021 23:16:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:16:40: 21000000 INFO @ Wed, 08 Dec 2021 23:16:41: 25000000 INFO @ Wed, 08 Dec 2021 23:16:48: 22000000 INFO @ Wed, 08 Dec 2021 23:16:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:16:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:16:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.05_summits.bed INFO @ Wed, 08 Dec 2021 23:16:48: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5805 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:16:49: 26000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:16:55: 23000000 INFO @ Wed, 08 Dec 2021 23:16:56: #1 tag size is determined as 125 bps INFO @ Wed, 08 Dec 2021 23:16:56: #1 tag size = 125 INFO @ Wed, 08 Dec 2021 23:16:56: #1 total tags in treatment: 11214676 INFO @ Wed, 08 Dec 2021 23:16:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:16:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:16:56: #1 tags after filtering in treatment: 8190678 INFO @ Wed, 08 Dec 2021 23:16:56: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 08 Dec 2021 23:16:56: #1 finished! INFO @ Wed, 08 Dec 2021 23:16:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:16:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:16:56: #2 number of paired peaks: 733 WARNING @ Wed, 08 Dec 2021 23:16:56: Fewer paired peaks (733) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 733 pairs to build model! INFO @ Wed, 08 Dec 2021 23:16:56: start model_add_line... INFO @ Wed, 08 Dec 2021 23:16:57: start X-correlation... INFO @ Wed, 08 Dec 2021 23:16:57: end of X-cor INFO @ Wed, 08 Dec 2021 23:16:57: #2 finished! INFO @ Wed, 08 Dec 2021 23:16:57: #2 predicted fragment length is 210 bps INFO @ Wed, 08 Dec 2021 23:16:57: #2 alternative fragment length(s) may be 210 bps INFO @ Wed, 08 Dec 2021 23:16:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.10_model.r WARNING @ Wed, 08 Dec 2021 23:16:57: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:16:57: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Wed, 08 Dec 2021 23:16:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:16:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:16:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:17:02: 24000000 INFO @ Wed, 08 Dec 2021 23:17:09: 25000000 INFO @ Wed, 08 Dec 2021 23:17:13: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:17:16: 26000000 INFO @ Wed, 08 Dec 2021 23:17:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:17:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:17:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.10_summits.bed INFO @ Wed, 08 Dec 2021 23:17:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3374 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:17:23: #1 tag size is determined as 125 bps INFO @ Wed, 08 Dec 2021 23:17:23: #1 tag size = 125 INFO @ Wed, 08 Dec 2021 23:17:23: #1 total tags in treatment: 11214676 INFO @ Wed, 08 Dec 2021 23:17:23: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:17:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:17:23: #1 tags after filtering in treatment: 8190678 INFO @ Wed, 08 Dec 2021 23:17:23: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 08 Dec 2021 23:17:23: #1 finished! INFO @ Wed, 08 Dec 2021 23:17:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:17:24: #2 number of paired peaks: 733 WARNING @ Wed, 08 Dec 2021 23:17:24: Fewer paired peaks (733) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 733 pairs to build model! INFO @ Wed, 08 Dec 2021 23:17:24: start model_add_line... INFO @ Wed, 08 Dec 2021 23:17:24: start X-correlation... INFO @ Wed, 08 Dec 2021 23:17:24: end of X-cor INFO @ Wed, 08 Dec 2021 23:17:24: #2 finished! INFO @ Wed, 08 Dec 2021 23:17:24: #2 predicted fragment length is 210 bps INFO @ Wed, 08 Dec 2021 23:17:24: #2 alternative fragment length(s) may be 210 bps INFO @ Wed, 08 Dec 2021 23:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.20_model.r WARNING @ Wed, 08 Dec 2021 23:17:24: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:17:24: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Wed, 08 Dec 2021 23:17:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:17:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:17:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:17:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:17:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:17:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845648/SRX8845648.20_summits.bed INFO @ Wed, 08 Dec 2021 23:17:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1480 records, 4 fields): 3 millis CompletedMACS2peakCalling