[2024-01-25 18:49:50,928] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:50,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:50,933] [INFO] DQC Reference Directory: /var/lib/cwl/stgff77cd2f-4582-4517-8ec8-cb2151443b5d/dqc_reference
[2024-01-25 18:49:52,106] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:52,107] [INFO] Task started: Prodigal
[2024-01-25 18:49:52,107] [INFO] Running command: gunzip -c /var/lib/cwl/stgada13368-5dfd-4f4b-af63-1ac391d692fd/GCF_004011175.1_ASM401117v1_genomic.fna.gz | prodigal -d GCF_004011175.1_ASM401117v1_genomic.fna/cds.fna -a GCF_004011175.1_ASM401117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:02,132] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:02,133] [INFO] Task started: HMMsearch
[2024-01-25 18:50:02,133] [INFO] Running command: hmmsearch --tblout GCF_004011175.1_ASM401117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff77cd2f-4582-4517-8ec8-cb2151443b5d/dqc_reference/reference_markers.hmm GCF_004011175.1_ASM401117v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:02,347] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:02,348] [INFO] Found 6/6 markers.
[2024-01-25 18:50:02,378] [INFO] Query marker FASTA was written to GCF_004011175.1_ASM401117v1_genomic.fna/markers.fasta
[2024-01-25 18:50:02,379] [INFO] Task started: Blastn
[2024-01-25 18:50:02,379] [INFO] Running command: blastn -query GCF_004011175.1_ASM401117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff77cd2f-4582-4517-8ec8-cb2151443b5d/dqc_reference/reference_markers.fasta -out GCF_004011175.1_ASM401117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:03,184] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:03,187] [INFO] Selected 31 target genomes.
[2024-01-25 18:50:03,187] [INFO] Target genome list was writen to GCF_004011175.1_ASM401117v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:03,210] [INFO] Task started: fastANI
[2024-01-25 18:50:03,210] [INFO] Running command: fastANI --query /var/lib/cwl/stgada13368-5dfd-4f4b-af63-1ac391d692fd/GCF_004011175.1_ASM401117v1_genomic.fna.gz --refList GCF_004011175.1_ASM401117v1_genomic.fna/target_genomes.txt --output GCF_004011175.1_ASM401117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:26,148] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:26,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff77cd2f-4582-4517-8ec8-cb2151443b5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:26,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff77cd2f-4582-4517-8ec8-cb2151443b5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:26,166] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:50:26,166] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:50:26,166] [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
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	79.2151	516	1312	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.1689	540	1312	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	79.1237	511	1312	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	78.95	480	1312	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	78.9438	486	1312	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.7174	520	1312	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.7012	467	1312	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.6538	468	1312	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	78.6313	475	1312	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	78.5906	455	1312	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	78.5792	452	1312	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.4727	383	1312	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.4673	427	1312	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4435	420	1312	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.4177	437	1312	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	78.3913	423	1312	95	below_threshold
Roseitranquillus sediminis	strain=MCCB 386	GCA_016918935.1	2809051	2809051	type	True	78.3457	373	1312	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	78.343	338	1312	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.3283	364	1312	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.3113	507	1312	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	78.2873	490	1312	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	78.2056	352	1312	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.1684	410	1312	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	78.1596	470	1312	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.1423	447	1312	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	78.0595	362	1312	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.0451	449	1312	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	78.0138	402	1312	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	77.996	405	1312	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.9362	405	1312	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	77.7757	356	1312	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:26,167] [INFO] DFAST Taxonomy check result was written to GCF_004011175.1_ASM401117v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:26,168] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:26,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:26,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff77cd2f-4582-4517-8ec8-cb2151443b5d/dqc_reference/checkm_data
[2024-01-25 18:50:26,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:26,207] [INFO] Task started: CheckM
[2024-01-25 18:50:26,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004011175.1_ASM401117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004011175.1_ASM401117v1_genomic.fna/checkm_input GCF_004011175.1_ASM401117v1_genomic.fna/checkm_result
[2024-01-25 18:50:58,869] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:58,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:58,891] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:58,891] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:58,891] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004011175.1_ASM401117v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:58,892] [INFO] Task started: Blastn
[2024-01-25 18:50:58,892] [INFO] Running command: blastn -query GCF_004011175.1_ASM401117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff77cd2f-4582-4517-8ec8-cb2151443b5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004011175.1_ASM401117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:00,318] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:00,321] [INFO] Selected 22 target genomes.
[2024-01-25 18:51:00,322] [INFO] Target genome list was writen to GCF_004011175.1_ASM401117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:00,346] [INFO] Task started: fastANI
[2024-01-25 18:51:00,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgada13368-5dfd-4f4b-af63-1ac391d692fd/GCF_004011175.1_ASM401117v1_genomic.fna.gz --refList GCF_004011175.1_ASM401117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004011175.1_ASM401117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:18,284] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:18,297] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:18,297] [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_004011175.1	s__Tranquillimonas littorinae	100.0	1310	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900115595.1	s__Tranquillimonas alkanivorans	79.8242	596	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	79.3217	556	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111315.1	s__Tranquillimonas rosea	79.311	583	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.2898	486	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141995.1	s__Palleronia salina	79.1971	517	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_900172315.1	s__Palleronia marisminoris	78.9311	482	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCA_019061145.1	s__ASV31 sp019061145	78.8973	468	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004005435.1	s__CCMM004 sp004005435	78.8102	521	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CCMM004	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	78.7736	531	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	78.7492	516	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358695.1	s__Palleronia sp004358695	78.6872	468	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762635.1	s__JABURR01 sp014762635	78.5935	394	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	78.4333	485	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.4183	408	1312	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_003340565.1	s__HLUCCA09 sp003340565	78.2341	433	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314805.1	s__Roseicyclus sp001314805	78.2235	373	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.2203	455	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003605175.1	s__IMCC34051 sp003605175	78.1968	433	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	78.1577	474	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003298775.1	s__Rhodosalinus sp003298775	78.0624	432	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109195.1	s__Pseudooceanicola nitratireducens	77.9953	405	1312	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:18,299] [INFO] GTDB search result was written to GCF_004011175.1_ASM401117v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:18,299] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:18,304] [INFO] DFAST_QC result json was written to GCF_004011175.1_ASM401117v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:18,304] [INFO] DFAST_QC completed!
[2024-01-25 18:51:18,304] [INFO] Total running time: 0h1m27s