@HD	VN:1.6	SO:coordinate
@SQ	SN:chr2L	LN:23513712
@SQ	SN:chr2R	LN:25286936
@PG	PN:minimap2	ID:minimap2	VN:2.30-r1287	CL:minimap2 -ax map-ont -y -t 14 /home/user/project/reference/dm6_chr.fa -
@PG	PN:samtools	ID:samtools	VN:1.21	PP:minimap2	CL:samtools sort -@8 -m2G -o /home/user/project/data/fiber-seq/timecourse/bam_tmp/sample_A_3-4.5hr.aligned.sorted.bam -
@PG	PN:fiberhmm-call	ID:fiberhmm-call	VN:2.16.3	PP:samtools	DS:FiberHMM fused apply+recall; coord=molecular (ns/nl/as/al/MA in molecular original-fiber coordinates); mode=nanopore-fiber recall_nucs=True phase_nrl=191 chimera_filter=n/a dedup=off	CL:/home/user/miniconda3/bin/fiberhmm-call -i /home/user/project/data/fiber-seq/timecourse/bam_tmp/sample_A_3-4.5hr.aligned.sorted.bam -o /home/user/project/data/fiber-seq/timecourse/bam/sample_A_3-4.5hr.fiberhmm.thr248.bam --enzyme hia5 --seq nanopore --prob-threshold 248 --region-parallel --skip-scaffolds -c 12 --io-threads 8
@PG	PN:samtools	ID:samtools.1	VN:1.21	PP:fiberhmm-call	CL:samtools cat -h /home/user/project/data/fiber-seq/timecourse/bam/.fiberhmm_call_tmp_b2s0mlkt/region_000000.bam -b /home/user/project/data/fiber-seq/timecourse/bam/.fiberhmm_call_tmp_b2s0mlkt/bam_list.txt -o /home/user/project/data/fiber-seq/timecourse/bam/sample_A_3-4.5hr.fiberhmm.thr248.bam
@PG	PN:samtools	ID:samtools.2	VN:1.21	PP:samtools.1	CL:samtools view -@ 8 -b -x ns,nl,as,al,nq,aq,MA,AQ,AN -o /data/fiberhmm_ont_topology_v2.16.7/WT_3-4.5hr/WT_3-4.5hr.aligned.mmml.clean.bam /data/fiberhmm_ont_topology_v2.16.7/WT_3-4.5hr/WT_3-4.5hr.source.fiberhmm.thr248.bam
@PG	PN:fiberhmm-call	ID:fiberhmm-call.2	VN:2.16.7	PP:samtools.2	DS:FiberHMM fused apply+recall; coord=molecular (ns/nl/as/al/MA in molecular original-fiber coordinates); mode=nanopore-fiber recall_nucs=True nuc_recall_policy=topology phase_nrl=0 chimera_filter=n/a dedup=off	CL:/tmp/fiberhmm-release-2.16.7/fiberhmm/cli/call.py --input /data/fiberhmm_ont_topology_v2.16.7/WT_3-4.5hr/WT_3-4.5hr.aligned.mmml.clean.bam --output /data/fiberhmm_ont_topology_v2.16.7/WT_3-4.5hr/WT_3-4.5hr.fiberhmm.v2.16.7.thr248.topology.bam --enzyme hia5 --seq nanopore --prob-threshold 248 --recall-nucs --nuc-recall-policy topology --phase-nrl off --msp-min-size 60 --region-parallel --skip-scaffolds --cores 12 --io-threads 8
@PG	PN:samtools	ID:samtools.3	VN:1.21	PP:fiberhmm-call.2	CL:samtools cat -h /data/fiberhmm_ont_topology_v2.16.7/WT_3-4.5hr/.fiberhmm_call_tmp_4xrctgu_/region_000000.bam -b /data/fiberhmm_ont_topology_v2.16.7/WT_3-4.5hr/.fiberhmm_call_tmp_4xrctgu_/bam_list.txt -o /data/fiberhmm_ont_topology_v2.16.7/WT_3-4.5hr/WT_3-4.5hr.fiberhmm.v2.16.7.thr248.topology.bam
@PG	PN:samtools	ID:samtools.4	VN:1.21	PP:samtools.3	CL:samtools view -@ 2 -h -b -x ns,nl,as,al,nq,aq,MA,AQ,AN,mq,lq,rq,tn,tl,tq,el,er -o runs/ont_hia5_late/input/ont_hia5_late.chr2L.clean.bam /data/fiber-seq data/embryo/timecourse/bam/topology_v2.16.7/WT_3-4.5hr.fiberhmm.v2.16.7.thr248.topology.bam chr2L:3000001-3050000
@PG	PN:samtools	ID:samtools.5	VN:1.21	PP:samtools.4	CL:samtools cat -o runs/ont_hia5_late/input/ont_hia5_late.4windows.clean.bam runs/ont_hia5_late/input/ont_hia5_late.chr2L.clean.bam runs/ont_hia5_late/input/ont_hia5_late.chr2R.clean.bam runs/ont_hia5_late/input/ont_hia5_late.chr3L.clean.bam runs/ont_hia5_late/input/ont_hia5_late.chr3R.clean.bam
@PG	PN:fiberhmm-call	ID:fiberhmm-call.3	VN:2.16.8	PP:samtools.5	DS:FiberHMM fused apply+recall; coord=molecular (ns/nl/as/al/MA in molecular original-fiber coordinates); mode=nanopore-fiber enzyme=hia5 tf_decoder=multi_interval_v1 tf_interval_penalty=5.0 recall_nucs=True nuc_recall_policy=topology nuc_profile=off nuc_sha256=off phase_nrl=0 ddda_derived_tf_edge_gap=off chimera_filter=n/a dedup=off daf_snp_mask=off daf_run_mask=off ddda_mcg=off	CL:/home/user/work/frozen_dc7abba_p29/fiberhmm/cli/call.py -i /home/user/work dir/runs/ont_hia5_late/input/ont_hia5_late.4windows.clean.bam -o /home/user/work/ont_run/fixed_dc7abba/ont_hia5.full.bam --enzyme hia5 --seq nanopore --prob-threshold 248 --nuc-recall-policy topology --phase-nrl off --msp-min-size 60 --primary --with-scores --no-qc --no-dedup --recall-nucs -c 4 --io-threads 1
@CO	FIBERHMM-CHEMISTRY:v1:assay=fiber-seq;enzyme=hia5;platform=nanopore;mode=nanopore-fiber;model=hia5_nanopore
@CO	MA-TYPES:v1:nuc,msp,tf
