[2024-01-24 13:19:01,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:01,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:01,322] [INFO] DQC Reference Directory: /var/lib/cwl/stge3661064-97a1-4e30-9260-86ca43fabe19/dqc_reference
[2024-01-24 13:19:02,704] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:02,705] [INFO] Task started: Prodigal
[2024-01-24 13:19:02,705] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a4bfecb-b502-4d93-8c7b-67cff87b0aab/GCF_014201715.1_ASM1420171v1_genomic.fna.gz | prodigal -d GCF_014201715.1_ASM1420171v1_genomic.fna/cds.fna -a GCF_014201715.1_ASM1420171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:36,532] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:36,533] [INFO] Task started: HMMsearch
[2024-01-24 13:19:36,533] [INFO] Running command: hmmsearch --tblout GCF_014201715.1_ASM1420171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3661064-97a1-4e30-9260-86ca43fabe19/dqc_reference/reference_markers.hmm GCF_014201715.1_ASM1420171v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:36,829] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:36,831] [INFO] Found 6/6 markers.
[2024-01-24 13:19:36,877] [INFO] Query marker FASTA was written to GCF_014201715.1_ASM1420171v1_genomic.fna/markers.fasta
[2024-01-24 13:19:36,878] [INFO] Task started: Blastn
[2024-01-24 13:19:36,878] [INFO] Running command: blastn -query GCF_014201715.1_ASM1420171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3661064-97a1-4e30-9260-86ca43fabe19/dqc_reference/reference_markers.fasta -out GCF_014201715.1_ASM1420171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:37,532] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:37,536] [INFO] Selected 11 target genomes.
[2024-01-24 13:19:37,536] [INFO] Target genome list was writen to GCF_014201715.1_ASM1420171v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:37,555] [INFO] Task started: fastANI
[2024-01-24 13:19:37,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a4bfecb-b502-4d93-8c7b-67cff87b0aab/GCF_014201715.1_ASM1420171v1_genomic.fna.gz --refList GCF_014201715.1_ASM1420171v1_genomic.fna/target_genomes.txt --output GCF_014201715.1_ASM1420171v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:47,392] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:47,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3661064-97a1-4e30-9260-86ca43fabe19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:47,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3661064-97a1-4e30-9260-86ca43fabe19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:47,399] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:47,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:47,400] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Haloferula luteola	strain=YC6886	GCA_014201715.1	595692	595692	type	True	100.0	1585	1589	95	conclusive
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	77.398	203	1589	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	77.3132	128	1589	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	76.9495	150	1589	95	below_threshold
Luteolibacter pohnpeiensis	strain=KCTC 22041	GCA_016595435.1	454153	454153	type	True	76.8348	73	1589	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	76.589	104	1589	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:47,401] [INFO] DFAST Taxonomy check result was written to GCF_014201715.1_ASM1420171v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:47,402] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:47,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:47,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3661064-97a1-4e30-9260-86ca43fabe19/dqc_reference/checkm_data
[2024-01-24 13:19:47,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:47,447] [INFO] Task started: CheckM
[2024-01-24 13:19:47,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201715.1_ASM1420171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201715.1_ASM1420171v1_genomic.fna/checkm_input GCF_014201715.1_ASM1420171v1_genomic.fna/checkm_result
[2024-01-24 13:21:18,205] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:18,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:18,222] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:18,222] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:18,223] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201715.1_ASM1420171v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:18,223] [INFO] Task started: Blastn
[2024-01-24 13:21:18,223] [INFO] Running command: blastn -query GCF_014201715.1_ASM1420171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3661064-97a1-4e30-9260-86ca43fabe19/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201715.1_ASM1420171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:19,002] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:19,005] [INFO] Selected 13 target genomes.
[2024-01-24 13:21:19,005] [INFO] Target genome list was writen to GCF_014201715.1_ASM1420171v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:19,027] [INFO] Task started: fastANI
[2024-01-24 13:21:19,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a4bfecb-b502-4d93-8c7b-67cff87b0aab/GCF_014201715.1_ASM1420171v1_genomic.fna.gz --refList GCF_014201715.1_ASM1420171v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201715.1_ASM1420171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:29,760] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:29,780] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:29,780] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014201715.1	s__Haloferula luteola	100.0	1585	1589	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016595525.1	s__Haloferula rosea	77.3957	203	1589	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904755.1	s__Haloferula sp014904755	77.0765	223	1589	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293445.1	s__Haloferula sp004293445	77.0719	143	1589	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	99.99	99.98	0.97	0.96	4	-
GCA_003820635.1	s__Luteolibacter sp003820635	76.9787	90	1589	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969605.1	s__Luteolibacter sp018969605	76.9738	69	1589	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012913485.1	s__Haloferula lutea	76.9495	150	1589	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304315.1	s__Haloferula sp002304315	76.7813	126	1589	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739615.1	s__Haloferula sp000739615	76.78	164	1589	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016811075.1	s__UBA985 sp016811075	76.5142	53	1589	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	99.37	98.74	0.97	0.95	3	-
GCA_016795385.1	s__Arctic95D-9 sp016795385	76.3813	54	1589	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:29,781] [INFO] GTDB search result was written to GCF_014201715.1_ASM1420171v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:29,782] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:29,787] [INFO] DFAST_QC result json was written to GCF_014201715.1_ASM1420171v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:29,787] [INFO] DFAST_QC completed!
[2024-01-24 13:21:29,787] [INFO] Total running time: 0h2m28s