[2024-01-24 13:49:13,569] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:13,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:13,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg84c64369-9c3f-4d5a-ad8e-ab72193593ef/dqc_reference
[2024-01-24 13:49:14,926] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:14,927] [INFO] Task started: Prodigal
[2024-01-24 13:49:14,927] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b3effe6-ae2a-4ff6-96af-e04f48af11d6/GCF_002109495.1_ASM210949v1_genomic.fna.gz | prodigal -d GCF_002109495.1_ASM210949v1_genomic.fna/cds.fna -a GCF_002109495.1_ASM210949v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:32,969] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:32,970] [INFO] Task started: HMMsearch
[2024-01-24 13:49:32,970] [INFO] Running command: hmmsearch --tblout GCF_002109495.1_ASM210949v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84c64369-9c3f-4d5a-ad8e-ab72193593ef/dqc_reference/reference_markers.hmm GCF_002109495.1_ASM210949v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:33,253] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:33,254] [INFO] Found 6/6 markers.
[2024-01-24 13:49:33,295] [INFO] Query marker FASTA was written to GCF_002109495.1_ASM210949v1_genomic.fna/markers.fasta
[2024-01-24 13:49:33,295] [INFO] Task started: Blastn
[2024-01-24 13:49:33,300] [INFO] Running command: blastn -query GCF_002109495.1_ASM210949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84c64369-9c3f-4d5a-ad8e-ab72193593ef/dqc_reference/reference_markers.fasta -out GCF_002109495.1_ASM210949v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:34,020] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:34,024] [INFO] Selected 30 target genomes.
[2024-01-24 13:49:34,025] [INFO] Target genome list was writen to GCF_002109495.1_ASM210949v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:34,052] [INFO] Task started: fastANI
[2024-01-24 13:49:34,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b3effe6-ae2a-4ff6-96af-e04f48af11d6/GCF_002109495.1_ASM210949v1_genomic.fna.gz --refList GCF_002109495.1_ASM210949v1_genomic.fna/target_genomes.txt --output GCF_002109495.1_ASM210949v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:00,096] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:00,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84c64369-9c3f-4d5a-ad8e-ab72193593ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:00,097] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84c64369-9c3f-4d5a-ad8e-ab72193593ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:00,115] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:00,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:00,115] [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
Magnetofaba australis	strain=IT-1	GCA_002109495.1	1472297	1472297	type	True	100.0	1652	1653	95	conclusive
Magnetococcus marinus	strain=MC-1	GCA_000014865.1	1124597	1124597	type	True	76.7475	118	1653	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.6471	128	1653	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.449	107	1653	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.264	101	1653	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.1758	95	1653	95	below_threshold
Sulfuricaulis limicola	strain=HA5	GCA_002355735.1	1620215	1620215	type	True	76.1657	55	1653	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.1108	90	1653	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	76.038	77	1653	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.8513	108	1653	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	75.8222	76	1653	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	75.7286	82	1653	95	below_threshold
Geminicoccus roseus	strain=DSM 18922	GCA_000427665.1	404900	404900	type	True	75.711	82	1653	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.6817	113	1653	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	75.653	103	1653	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.6348	67	1653	95	below_threshold
Pseudomonas oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	75.5457	71	1653	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	75.5381	88	1653	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.4606	104	1653	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	75.361	69	1653	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	75.2753	51	1653	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	75.2648	53	1653	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	75.1716	52	1653	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,117] [INFO] DFAST Taxonomy check result was written to GCF_002109495.1_ASM210949v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:00,117] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:00,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:00,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84c64369-9c3f-4d5a-ad8e-ab72193593ef/dqc_reference/checkm_data
[2024-01-24 13:50:00,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:00,169] [INFO] Task started: CheckM
[2024-01-24 13:50:00,169] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002109495.1_ASM210949v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002109495.1_ASM210949v1_genomic.fna/checkm_input GCF_002109495.1_ASM210949v1_genomic.fna/checkm_result
[2024-01-24 13:50:51,902] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:51,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:51,922] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:51,923] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:51,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002109495.1_ASM210949v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:51,923] [INFO] Task started: Blastn
[2024-01-24 13:50:51,923] [INFO] Running command: blastn -query GCF_002109495.1_ASM210949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84c64369-9c3f-4d5a-ad8e-ab72193593ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_002109495.1_ASM210949v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:53,076] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:53,079] [INFO] Selected 26 target genomes.
[2024-01-24 13:50:53,080] [INFO] Target genome list was writen to GCF_002109495.1_ASM210949v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:53,127] [INFO] Task started: fastANI
[2024-01-24 13:50:53,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b3effe6-ae2a-4ff6-96af-e04f48af11d6/GCF_002109495.1_ASM210949v1_genomic.fna.gz --refList GCF_002109495.1_ASM210949v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002109495.1_ASM210949v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:13,835] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:13,848] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:13,849] [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_002109495.1	s__Magnetofaba australis	100.0	1652	1653	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetococcaceae;g__Magnetofaba	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000014865.1	s__Magnetococcus marinus	76.8647	118	1653	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetococcaceae;g__Magnetococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002753665.1	s__DC0425bin3 sp002753665	76.8302	202	1653	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__DC0425bin3;g__DC0425bin3	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000377945.1	s__Thioalkalivibrio_A sulfidiphilus_A	76.6993	94	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	76.6479	128	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015231925.1	s__JADGAQ01 sp015231925	76.4685	134	1653	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__JADGAQ01;g__JADGAQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015231775.1	s__JAANAU01 sp015231775	76.4652	122	1653	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetaquicoccaceae;g__JAANAU01	95.0	97.81	97.81	0.75	0.75	2	-
GCA_015232245.1	s__JAANAU01 sp015232245	76.4424	106	1653	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetaquicoccaceae;g__JAANAU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	76.2964	106	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234115.1	s__JAANAU01 sp015234115	76.1118	100	1653	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetaquicoccaceae;g__JAANAU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002753495.1	s__HA3dbin3 sp002753495	76.0442	91	1653	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__DC0425bin3;g__HA3dbin3	95.0	99.85	99.85	0.94	0.94	2	-
GCF_005887635.2	s__Paroceanicella profunda	75.8745	78	1653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295635.1	s__S0819 sp009295635	75.8564	80	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__S0819	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014192275.1	s__Halomonas stenophila	75.8247	76	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015231295.1	s__JAANAU01 sp015231295	75.7824	98	1653	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetaquicoccaceae;g__JAANAU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001945395.1	s__Pseudomonas_E sp001945395	75.5181	65	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:13,851] [INFO] GTDB search result was written to GCF_002109495.1_ASM210949v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:13,851] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:13,856] [INFO] DFAST_QC result json was written to GCF_002109495.1_ASM210949v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:13,856] [INFO] DFAST_QC completed!
[2024-01-24 13:51:13,856] [INFO] Total running time: 0h2m0s