[2024-01-24 11:05:03,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg29143cfb-be5c-41ab-a8d4-689be74e670b/dqc_reference
[2024-01-24 11:05:05,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,765] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,765] [INFO] Running command: gunzip -c /var/lib/cwl/stga757d12e-6aef-43b8-b11c-a2f35a8ed74d/GCF_001580045.1_ASM158004v1_genomic.fna.gz | prodigal -d GCF_001580045.1_ASM158004v1_genomic.fna/cds.fna -a GCF_001580045.1_ASM158004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:15,930] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:15,930] [INFO] Task started: HMMsearch
[2024-01-24 11:05:15,930] [INFO] Running command: hmmsearch --tblout GCF_001580045.1_ASM158004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29143cfb-be5c-41ab-a8d4-689be74e670b/dqc_reference/reference_markers.hmm GCF_001580045.1_ASM158004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:16,163] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:16,164] [INFO] Found 6/6 markers.
[2024-01-24 11:05:16,189] [INFO] Query marker FASTA was written to GCF_001580045.1_ASM158004v1_genomic.fna/markers.fasta
[2024-01-24 11:05:16,189] [INFO] Task started: Blastn
[2024-01-24 11:05:16,190] [INFO] Running command: blastn -query GCF_001580045.1_ASM158004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29143cfb-be5c-41ab-a8d4-689be74e670b/dqc_reference/reference_markers.fasta -out GCF_001580045.1_ASM158004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:16,919] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:16,921] [INFO] Selected 9 target genomes.
[2024-01-24 11:05:16,922] [INFO] Target genome list was writen to GCF_001580045.1_ASM158004v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:16,928] [INFO] Task started: fastANI
[2024-01-24 11:05:16,928] [INFO] Running command: fastANI --query /var/lib/cwl/stga757d12e-6aef-43b8-b11c-a2f35a8ed74d/GCF_001580045.1_ASM158004v1_genomic.fna.gz --refList GCF_001580045.1_ASM158004v1_genomic.fna/target_genomes.txt --output GCF_001580045.1_ASM158004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:24,448] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:24,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29143cfb-be5c-41ab-a8d4-689be74e670b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:24,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29143cfb-be5c-41ab-a8d4-689be74e670b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:24,455] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:24,456] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:24,456] [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
Cephaloticoccus capnophilus	strain=CV41	GCA_001580045.1	1548208	1548208	type	True	100.0	664	669	95	conclusive
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	80.6833	420	669	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	77.6926	108	669	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	77.3418	109	669	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.2641	118	669	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	77.2306	105	669	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	77.2167	104	669	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:24,457] [INFO] DFAST Taxonomy check result was written to GCF_001580045.1_ASM158004v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:24,457] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:24,457] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:24,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29143cfb-be5c-41ab-a8d4-689be74e670b/dqc_reference/checkm_data
[2024-01-24 11:05:24,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:24,485] [INFO] Task started: CheckM
[2024-01-24 11:05:24,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001580045.1_ASM158004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001580045.1_ASM158004v1_genomic.fna/checkm_input GCF_001580045.1_ASM158004v1_genomic.fna/checkm_result
[2024-01-24 11:05:54,235] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:54,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:54,251] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:54,251] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:54,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001580045.1_ASM158004v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:54,251] [INFO] Task started: Blastn
[2024-01-24 11:05:54,251] [INFO] Running command: blastn -query GCF_001580045.1_ASM158004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29143cfb-be5c-41ab-a8d4-689be74e670b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001580045.1_ASM158004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:55,416] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:55,419] [INFO] Selected 20 target genomes.
[2024-01-24 11:05:55,419] [INFO] Target genome list was writen to GCF_001580045.1_ASM158004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:55,473] [INFO] Task started: fastANI
[2024-01-24 11:05:55,473] [INFO] Running command: fastANI --query /var/lib/cwl/stga757d12e-6aef-43b8-b11c-a2f35a8ed74d/GCF_001580045.1_ASM158004v1_genomic.fna.gz --refList GCF_001580045.1_ASM158004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001580045.1_ASM158004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:09,574] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:09,584] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:09,584] [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_001580045.1	s__Cephaloticoccus capnophilus	100.0	664	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Cephaloticoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001580015.1	s__Cephaloticoccus primus	80.7124	418	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Cephaloticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715765.1	s__UBA2377 sp016715765	77.7618	126	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344205.1	s__UBA2377 sp002344205	77.6252	132	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	99.84	99.84	0.94	0.94	2	-
GCA_903872505.1	s__Opi-474 sp903872505	77.3344	130	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.99	99.98	0.99	0.99	3	-
GCA_001650175.1	s__Ereboglobus sp001650175	77.3198	130	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Ereboglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299415.1	s__CAIYFD01 sp900299415	77.3167	69	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIYFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903825285.1	s__Opi-474 sp903825285	77.3156	125	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.78	99.55	0.96	0.94	12	-
GCA_016217545.1	s__Didemnitutus sp016217545	77.3144	117	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903902745.1	s__CAIUWA01 sp903902745	77.0678	109	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIUWA01	95.0	99.98	99.98	0.98	0.97	4	-
GCA_016235555.1	s__ER46 sp016235555	77.0277	149	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903830425.1	s__Opi-474 sp903830425	77.0045	131	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.49	99.28	0.91	0.87	25	-
GCA_018239675.1	s__Opi-474 sp018239675	76.9215	97	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002382525.1	s__Rariglobus sp002382525	76.8547	98	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	99.24	99.24	0.83	0.83	2	-
GCA_903948415.1	s__CAITWF01 sp903948415	76.8186	125	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737275.1	s__Tous-C4FEB sp002737275	76.3685	78	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:09,586] [INFO] GTDB search result was written to GCF_001580045.1_ASM158004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:09,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:09,589] [INFO] DFAST_QC result json was written to GCF_001580045.1_ASM158004v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:09,589] [INFO] DFAST_QC completed!
[2024-01-24 11:06:09,589] [INFO] Total running time: 0h1m6s