[2024-01-24 12:28:34,787] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:34,789] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:34,789] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfa9ef35-0f5f-45e4-9463-aa569835f272/dqc_reference
[2024-01-24 12:28:36,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:36,005] [INFO] Task started: Prodigal
[2024-01-24 12:28:36,005] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bb5dc93-6ec8-4526-869d-0b45379e8d06/GCF_004342065.1_ASM434206v1_genomic.fna.gz | prodigal -d GCF_004342065.1_ASM434206v1_genomic.fna/cds.fna -a GCF_004342065.1_ASM434206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:51,497] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:51,498] [INFO] Task started: HMMsearch
[2024-01-24 12:28:51,498] [INFO] Running command: hmmsearch --tblout GCF_004342065.1_ASM434206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfa9ef35-0f5f-45e4-9463-aa569835f272/dqc_reference/reference_markers.hmm GCF_004342065.1_ASM434206v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:51,784] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:51,786] [INFO] Found 6/6 markers.
[2024-01-24 12:28:51,829] [INFO] Query marker FASTA was written to GCF_004342065.1_ASM434206v1_genomic.fna/markers.fasta
[2024-01-24 12:28:51,829] [INFO] Task started: Blastn
[2024-01-24 12:28:51,829] [INFO] Running command: blastn -query GCF_004342065.1_ASM434206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfa9ef35-0f5f-45e4-9463-aa569835f272/dqc_reference/reference_markers.fasta -out GCF_004342065.1_ASM434206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:52,714] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:52,718] [INFO] Selected 25 target genomes.
[2024-01-24 12:28:52,718] [INFO] Target genome list was writen to GCF_004342065.1_ASM434206v1_genomic.fna/target_genomes.txt
[2024-01-24 12:28:52,750] [INFO] Task started: fastANI
[2024-01-24 12:28:52,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bb5dc93-6ec8-4526-869d-0b45379e8d06/GCF_004342065.1_ASM434206v1_genomic.fna.gz --refList GCF_004342065.1_ASM434206v1_genomic.fna/target_genomes.txt --output GCF_004342065.1_ASM434206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:11,490] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:11,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfa9ef35-0f5f-45e4-9463-aa569835f272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:11,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfa9ef35-0f5f-45e4-9463-aa569835f272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:11,511] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:11,511] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:11,511] [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
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	100.0	1645	1647	95	conclusive
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	81.9742	791	1647	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.5242	538	1647	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.3274	443	1647	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.2899	518	1647	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	78.2393	529	1647	95	below_threshold
Poseidonocella pacifica	strain=DSM 29316	GCA_900111875.1	871651	871651	type	True	78.1425	275	1647	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.1253	449	1647	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.0967	452	1647	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	78.0879	470	1647	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.0106	428	1647	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	78.0039	427	1647	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.9792	378	1647	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.9134	389	1647	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.9036	467	1647	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.8897	412	1647	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.8649	413	1647	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.8607	397	1647	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.6571	346	1647	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.5689	356	1647	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.3914	319	1647	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	77.3844	325	1647	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.1739	273	1647	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.1402	304	1647	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.1313	305	1647	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:11,513] [INFO] DFAST Taxonomy check result was written to GCF_004342065.1_ASM434206v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:11,513] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:11,513] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:11,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfa9ef35-0f5f-45e4-9463-aa569835f272/dqc_reference/checkm_data
[2024-01-24 12:29:11,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:11,562] [INFO] Task started: CheckM
[2024-01-24 12:29:11,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342065.1_ASM434206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342065.1_ASM434206v1_genomic.fna/checkm_input GCF_004342065.1_ASM434206v1_genomic.fna/checkm_result
[2024-01-24 12:29:58,901] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:58,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:58,929] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:58,930] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:58,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342065.1_ASM434206v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:58,930] [INFO] Task started: Blastn
[2024-01-24 12:29:58,930] [INFO] Running command: blastn -query GCF_004342065.1_ASM434206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfa9ef35-0f5f-45e4-9463-aa569835f272/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342065.1_ASM434206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:00,588] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:00,593] [INFO] Selected 18 target genomes.
[2024-01-24 12:30:00,594] [INFO] Target genome list was writen to GCF_004342065.1_ASM434206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:00,610] [INFO] Task started: fastANI
[2024-01-24 12:30:00,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bb5dc93-6ec8-4526-869d-0b45379e8d06/GCF_004342065.1_ASM434206v1_genomic.fna.gz --refList GCF_004342065.1_ASM434206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342065.1_ASM434206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:16,163] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:16,190] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:16,191] [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_004342065.1	s__Primorskyibacter sedentarius	100.0	1645	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003313245.1	s__Primorskyibacter marinus	81.9734	792	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	81.9009	830	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.5558	501	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	78.2496	529	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_900111875.1	s__Poseidonocella pacifica	78.1563	274	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	78.1469	522	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.1257	449	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014637725.1	s__Marivita lacus	78.0925	471	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210095.1	s__Marinibacterium profundimaris	78.0334	485	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156805.1	s__Roseivivax lentus	78.0125	426	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.9386	414	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.9053	410	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_013031405.1	s__Ruegeria sp013031405	77.8543	453	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260265.1	s__Roseovarius sp003260265	77.7921	359	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.4927	342	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_900302455.1	s__Ruegeria_E mediterranea	77.3932	319	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	99.84	99.84	0.96	0.96	2	-
GCF_009811755.1	s__Roseobacter cerasinus	77.3923	324	1647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:16,193] [INFO] GTDB search result was written to GCF_004342065.1_ASM434206v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:16,194] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:16,198] [INFO] DFAST_QC result json was written to GCF_004342065.1_ASM434206v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:16,198] [INFO] DFAST_QC completed!
[2024-01-24 12:30:16,198] [INFO] Total running time: 0h1m41s