[2024-01-25 18:39:50,686] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:50,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:50,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg25730368-d584-4277-9c08-de2c189a04de/dqc_reference
[2024-01-25 18:39:51,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:51,881] [INFO] Task started: Prodigal
[2024-01-25 18:39:51,881] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f29a4a6-98bd-4949-8e67-d988d899837a/GCF_000145255.1_ASM14525v1_genomic.fna.gz | prodigal -d GCF_000145255.1_ASM14525v1_genomic.fna/cds.fna -a GCF_000145255.1_ASM14525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:00,202] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:00,202] [INFO] Task started: HMMsearch
[2024-01-25 18:40:00,203] [INFO] Running command: hmmsearch --tblout GCF_000145255.1_ASM14525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25730368-d584-4277-9c08-de2c189a04de/dqc_reference/reference_markers.hmm GCF_000145255.1_ASM14525v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:00,437] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:00,438] [INFO] Found 6/6 markers.
[2024-01-25 18:40:00,466] [INFO] Query marker FASTA was written to GCF_000145255.1_ASM14525v1_genomic.fna/markers.fasta
[2024-01-25 18:40:00,466] [INFO] Task started: Blastn
[2024-01-25 18:40:00,466] [INFO] Running command: blastn -query GCF_000145255.1_ASM14525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25730368-d584-4277-9c08-de2c189a04de/dqc_reference/reference_markers.fasta -out GCF_000145255.1_ASM14525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:01,070] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:01,074] [INFO] Selected 27 target genomes.
[2024-01-25 18:40:01,074] [INFO] Target genome list was writen to GCF_000145255.1_ASM14525v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:01,122] [INFO] Task started: fastANI
[2024-01-25 18:40:01,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f29a4a6-98bd-4949-8e67-d988d899837a/GCF_000145255.1_ASM14525v1_genomic.fna.gz --refList GCF_000145255.1_ASM14525v1_genomic.fna/target_genomes.txt --output GCF_000145255.1_ASM14525v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:20,148] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:20,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25730368-d584-4277-9c08-de2c189a04de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:20,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25730368-d584-4277-9c08-de2c189a04de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:20,159] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:20,159] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:20,160] [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
Gallionella capsiferriformans	strain=ES-2	GCA_000145255.1	370405	370405	type	True	100.0	1052	1054	95	conclusive
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.5335	195	1054	95	below_threshold
Janthinobacterium tructae	strain=SNU WT3	GCA_006517255.1	2590869	2590869	type	True	77.394	58	1054	95	below_threshold
Ferriphaselus amnicola	strain=OYT1	GCA_000974685.2	1188319	1188319	type	True	77.2677	123	1054	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	77.1184	59	1054	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	76.5404	76	1054	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	76.2932	53	1054	95	below_threshold
Sulfuriferula multivorans	strain=TTN	GCA_003851125.1	1559896	1559896	type	True	76.0717	63	1054	95	below_threshold
Janthinobacterium violaceinigrum	strain=FT13W	GCA_009208555.1	2654252	2654252	type	True	75.9086	58	1054	95	below_threshold
Paludibacterium purpuratum	strain=CECT 8976	GCA_004363805.1	1144873	1144873	type	True	75.8295	52	1054	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	75.656	55	1054	95	below_threshold
Janthinobacterium lividum	strain=H-24	GCA_001758635.1	29581	29581	suspected-type	True	75.5437	53	1054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:20,161] [INFO] DFAST Taxonomy check result was written to GCF_000145255.1_ASM14525v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:20,163] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:20,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:20,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25730368-d584-4277-9c08-de2c189a04de/dqc_reference/checkm_data
[2024-01-25 18:40:20,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:20,201] [INFO] Task started: CheckM
[2024-01-25 18:40:20,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000145255.1_ASM14525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000145255.1_ASM14525v1_genomic.fna/checkm_input GCF_000145255.1_ASM14525v1_genomic.fna/checkm_result
[2024-01-25 18:40:48,289] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:48,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:48,309] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:48,309] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:48,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000145255.1_ASM14525v1_genomic.fna/markers.fasta)
[2024-01-25 18:40:48,310] [INFO] Task started: Blastn
[2024-01-25 18:40:48,310] [INFO] Running command: blastn -query GCF_000145255.1_ASM14525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25730368-d584-4277-9c08-de2c189a04de/dqc_reference/reference_markers_gtdb.fasta -out GCF_000145255.1_ASM14525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:49,234] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:49,237] [INFO] Selected 11 target genomes.
[2024-01-25 18:40:49,237] [INFO] Target genome list was writen to GCF_000145255.1_ASM14525v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:49,246] [INFO] Task started: fastANI
[2024-01-25 18:40:49,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f29a4a6-98bd-4949-8e67-d988d899837a/GCF_000145255.1_ASM14525v1_genomic.fna.gz --refList GCF_000145255.1_ASM14525v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000145255.1_ASM14525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:40:56,603] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:56,609] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:40:56,610] [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_000145255.1	s__Gallionella capsiferriformans	100.0	1051	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001801025.1	s__Gallionella sp001801025	91.1845	790	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.91	99.81	0.99	0.99	3	-
GCA_903885165.1	s__Gallionella sp903885165	79.6074	306	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.76	99.35	0.93	0.83	60	-
GCA_903861075.1	s__Gallionella sp903861075	79.2488	237	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.60	99.38	0.89	0.85	4	-
GCA_002381565.1	s__Gallionella sp002381565	79.2046	359	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	98.74	97.66	0.88	0.86	3	-
GCA_903915035.1	s__Gallionella sp903915035	78.7923	283	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.81	99.81	0.88	0.88	2	-
GCA_017880865.1	s__Gallionella sp017880865	77.557	214	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153155.1	s__Gallionella sp003153155	77.5174	196	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801055.1	s__Gallionella sp001801055	76.9534	118	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:40:56,611] [INFO] GTDB search result was written to GCF_000145255.1_ASM14525v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:40:56,611] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:40:56,614] [INFO] DFAST_QC result json was written to GCF_000145255.1_ASM14525v1_genomic.fna/dqc_result.json
[2024-01-25 18:40:56,614] [INFO] DFAST_QC completed!
[2024-01-25 18:40:56,614] [INFO] Total running time: 0h1m6s