[2024-01-24 13:57:30,213] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:30,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:30,216] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbc19e99-9bbb-4d7a-b500-723822cf25ee/dqc_reference
[2024-01-24 13:57:31,474] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:31,475] [INFO] Task started: Prodigal
[2024-01-24 13:57:31,476] [INFO] Running command: gunzip -c /var/lib/cwl/stg0307c75b-3eab-4f96-8a00-cb9e83c5be01/GCF_032595355.1_ASM3259535v1_genomic.fna.gz | prodigal -d GCF_032595355.1_ASM3259535v1_genomic.fna/cds.fna -a GCF_032595355.1_ASM3259535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:49,733] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:49,734] [INFO] Task started: HMMsearch
[2024-01-24 13:57:49,734] [INFO] Running command: hmmsearch --tblout GCF_032595355.1_ASM3259535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbc19e99-9bbb-4d7a-b500-723822cf25ee/dqc_reference/reference_markers.hmm GCF_032595355.1_ASM3259535v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:50,063] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:50,064] [INFO] Found 6/6 markers.
[2024-01-24 13:57:50,111] [INFO] Query marker FASTA was written to GCF_032595355.1_ASM3259535v1_genomic.fna/markers.fasta
[2024-01-24 13:57:50,111] [INFO] Task started: Blastn
[2024-01-24 13:57:50,112] [INFO] Running command: blastn -query GCF_032595355.1_ASM3259535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbc19e99-9bbb-4d7a-b500-723822cf25ee/dqc_reference/reference_markers.fasta -out GCF_032595355.1_ASM3259535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:50,967] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:50,970] [INFO] Selected 28 target genomes.
[2024-01-24 13:57:50,971] [INFO] Target genome list was writen to GCF_032595355.1_ASM3259535v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:51,003] [INFO] Task started: fastANI
[2024-01-24 13:57:51,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg0307c75b-3eab-4f96-8a00-cb9e83c5be01/GCF_032595355.1_ASM3259535v1_genomic.fna.gz --refList GCF_032595355.1_ASM3259535v1_genomic.fna/target_genomes.txt --output GCF_032595355.1_ASM3259535v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:11,731] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:11,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbc19e99-9bbb-4d7a-b500-723822cf25ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:11,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbc19e99-9bbb-4d7a-b500-723822cf25ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:11,754] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:11,754] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:11,754] [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
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.2836	489	1749	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.2202	419	1749	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.2102	428	1749	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.0866	515	1749	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.9929	478	1749	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.9888	497	1749	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	77.985	463	1749	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.8631	443	1749	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	77.8355	319	1749	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	77.8081	355	1749	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.7479	416	1749	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	77.7421	281	1749	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.7068	407	1749	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.6951	310	1749	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	77.6267	347	1749	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	77.6145	315	1749	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.6085	350	1749	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.4777	379	1749	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.2927	371	1749	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	77.2608	236	1749	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	77.2256	258	1749	95	below_threshold
Ruegeria conchae	strain=DSM 29317	GCA_003664205.1	981384	981384	suspected-type	True	77.2139	257	1749	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	77.1621	292	1749	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	77.0568	232	1749	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.9044	223	1749	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.8581	236	1749	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	76.7829	189	1749	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	76.4706	151	1749	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:11,756] [INFO] DFAST Taxonomy check result was written to GCF_032595355.1_ASM3259535v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:11,757] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:11,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:11,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbc19e99-9bbb-4d7a-b500-723822cf25ee/dqc_reference/checkm_data
[2024-01-24 13:58:11,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:11,811] [INFO] Task started: CheckM
[2024-01-24 13:58:11,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_032595355.1_ASM3259535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_032595355.1_ASM3259535v1_genomic.fna/checkm_input GCF_032595355.1_ASM3259535v1_genomic.fna/checkm_result
[2024-01-24 13:59:08,476] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:08,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:08,496] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:08,496] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:08,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_032595355.1_ASM3259535v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:08,497] [INFO] Task started: Blastn
[2024-01-24 13:59:08,497] [INFO] Running command: blastn -query GCF_032595355.1_ASM3259535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbc19e99-9bbb-4d7a-b500-723822cf25ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_032595355.1_ASM3259535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:09,732] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:09,735] [INFO] Selected 25 target genomes.
[2024-01-24 13:59:09,735] [INFO] Target genome list was writen to GCF_032595355.1_ASM3259535v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:09,751] [INFO] Task started: fastANI
[2024-01-24 13:59:09,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg0307c75b-3eab-4f96-8a00-cb9e83c5be01/GCF_032595355.1_ASM3259535v1_genomic.fna.gz --refList GCF_032595355.1_ASM3259535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_032595355.1_ASM3259535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:29,878] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:29,898] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:29,898] [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_000473225.1	s__Sedimentitalea nanhaiensis	79.4092	712	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016521575.1	s__Sedimentitalea sp016521575	78.9154	606	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	78.8598	478	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	78.7371	586	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	78.3105	363	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.2727	491	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.2236	425	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.0897	516	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	77.985	463	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.9824	498	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003667315.2	s__Tropicibacter sp003667315	77.9034	352	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500245.1	s__Ruegeria_B sp010500245	77.8992	447	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	77.8777	441	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.8604	403	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	77.8209	421	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_003316635.1	s__Roseovarius dicentrarchi	77.7541	280	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.7521	418	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	77.7323	415	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_900108275.1	s__Jhaorihella thermophila	77.7082	419	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	77.6814	390	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	77.6785	481	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762325.1	s__Roseovarius faecimaris	77.6146	315	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	77.3923	289	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCA_000158135.1	s__Ruegeria sp000158135	77.3608	346	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110425.1	s__Salinihabitans flavidus	77.1523	294	1749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salinihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:29,900] [INFO] GTDB search result was written to GCF_032595355.1_ASM3259535v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:29,901] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:29,906] [INFO] DFAST_QC result json was written to GCF_032595355.1_ASM3259535v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:29,906] [INFO] DFAST_QC completed!
[2024-01-24 13:59:29,906] [INFO] Total running time: 0h1m60s