[2024-01-24 11:05:03,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,934] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,934] [INFO] DQC Reference Directory: /var/lib/cwl/stgf44a5c45-5bbb-4c0b-a0fc-e1326bdd8018/dqc_reference
[2024-01-24 11:05:05,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,813] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,813] [INFO] Running command: gunzip -c /var/lib/cwl/stge01d6c4f-6835-481c-84c5-4c0888fff0a0/GCF_019930905.1_ASM1993090v1_genomic.fna.gz | prodigal -d GCF_019930905.1_ASM1993090v1_genomic.fna/cds.fna -a GCF_019930905.1_ASM1993090v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:09,746] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:09,746] [INFO] Task started: HMMsearch
[2024-01-24 11:05:09,746] [INFO] Running command: hmmsearch --tblout GCF_019930905.1_ASM1993090v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf44a5c45-5bbb-4c0b-a0fc-e1326bdd8018/dqc_reference/reference_markers.hmm GCF_019930905.1_ASM1993090v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:09,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:09,997] [INFO] Found 6/6 markers.
[2024-01-24 11:05:10,018] [INFO] Query marker FASTA was written to GCF_019930905.1_ASM1993090v1_genomic.fna/markers.fasta
[2024-01-24 11:05:10,018] [INFO] Task started: Blastn
[2024-01-24 11:05:10,018] [INFO] Running command: blastn -query GCF_019930905.1_ASM1993090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf44a5c45-5bbb-4c0b-a0fc-e1326bdd8018/dqc_reference/reference_markers.fasta -out GCF_019930905.1_ASM1993090v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:12,076] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:12,079] [INFO] Selected 11 target genomes.
[2024-01-24 11:05:12,080] [INFO] Target genome list was writen to GCF_019930905.1_ASM1993090v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:12,087] [INFO] Task started: fastANI
[2024-01-24 11:05:12,087] [INFO] Running command: fastANI --query /var/lib/cwl/stge01d6c4f-6835-481c-84c5-4c0888fff0a0/GCF_019930905.1_ASM1993090v1_genomic.fna.gz --refList GCF_019930905.1_ASM1993090v1_genomic.fna/target_genomes.txt --output GCF_019930905.1_ASM1993090v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:18,445] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:18,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf44a5c45-5bbb-4c0b-a0fc-e1326bdd8018/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:18,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf44a5c45-5bbb-4c0b-a0fc-e1326bdd8018/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:18,457] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:05:18,457] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:05:18,457] [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
Haemophilus aegyptius	strain=FDAARGOS_1478	GCA_019930905.1	197575	197575	type	True	100.0	661	664	95	inconclusive
Haemophilus aegyptius	strain=NCTC8502	GCA_900475885.1	197575	197575	type	True	99.9986	662	664	95	inconclusive
Haemophilus influenzae	strain=NCTC8143	GCA_001457655.1	727	727	type	True	96.85	573	664	95	inconclusive
Haemophilus influenzae	strain=FDAARGOS_1560	GCA_020736045.1	727	727	type	True	96.8173	574	664	95	inconclusive
Haemophilus haemolyticus	strain=CCUG 12834	GCA_001679045.1	726	726	type	True	91.5614	475	664	95	below_threshold
Haemophilus seminalis	strain=SZY H1	GCA_006384255.1	2582921	2582921	type	True	90.0389	469	664	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	79.6809	318	664	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:18,458] [INFO] DFAST Taxonomy check result was written to GCF_019930905.1_ASM1993090v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:18,459] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:18,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:18,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf44a5c45-5bbb-4c0b-a0fc-e1326bdd8018/dqc_reference/checkm_data
[2024-01-24 11:05:18,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:18,483] [INFO] Task started: CheckM
[2024-01-24 11:05:18,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019930905.1_ASM1993090v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019930905.1_ASM1993090v1_genomic.fna/checkm_input GCF_019930905.1_ASM1993090v1_genomic.fna/checkm_result
[2024-01-24 11:05:37,820] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:37,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:37,841] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:37,842] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:37,842] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019930905.1_ASM1993090v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:37,843] [INFO] Task started: Blastn
[2024-01-24 11:05:37,843] [INFO] Running command: blastn -query GCF_019930905.1_ASM1993090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf44a5c45-5bbb-4c0b-a0fc-e1326bdd8018/dqc_reference/reference_markers_gtdb.fasta -out GCF_019930905.1_ASM1993090v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:39,404] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:39,412] [INFO] Selected 11 target genomes.
[2024-01-24 11:05:39,413] [INFO] Target genome list was writen to GCF_019930905.1_ASM1993090v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:39,420] [INFO] Task started: fastANI
[2024-01-24 11:05:39,420] [INFO] Running command: fastANI --query /var/lib/cwl/stge01d6c4f-6835-481c-84c5-4c0888fff0a0/GCF_019930905.1_ASM1993090v1_genomic.fna.gz --refList GCF_019930905.1_ASM1993090v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019930905.1_ASM1993090v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:05:44,890] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:44,898] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:05:44,898] [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_900475885.1	s__Haemophilus aegyptius	99.9986	659	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.9609	98.11	97.16	0.93	0.88	31	conclusive
GCF_001457655.1	s__Haemophilus influenzae	96.8293	575	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.9609	97.88	97.07	0.94	0.87	511	-
GCF_004802395.1	s__Haemophilus influenzae_E	96.6229	556	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.8621	97.44	97.09	0.92	0.89	88	-
GCF_002989035.1	s__Haemophilus influenzae_F	96.2531	457	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.9474	98.22	97.14	0.92	0.83	74	-
GCF_900475755.1	s__Haemophilus influenzae_D	94.7836	541	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.4263	96.90	95.46	0.91	0.81	69	-
GCF_000222025.1	s__Haemophilus haemolyticus_G	92.6622	487	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003493605.1	s__Haemophilus haemolyticus_J	92.5007	493	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352385.1	s__Haemophilus haemolyticus_I	91.8327	495	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	95.71	95.22	0.89	0.82	17	-
GCF_001276515.1	s__Haemophilus sp001276515	91.8251	483	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	95.49	95.48	0.91	0.90	3	-
GCF_001679045.1	s__Haemophilus haemolyticus	91.5346	476	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	95.67	95.07	0.90	0.84	29	-
GCF_014931275.1	s__Haemophilus_D sp900755445	81.2469	318	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	96.11	95.22	0.94	0.92	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:05:44,899] [INFO] GTDB search result was written to GCF_019930905.1_ASM1993090v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:05:44,900] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:05:44,903] [INFO] DFAST_QC result json was written to GCF_019930905.1_ASM1993090v1_genomic.fna/dqc_result.json
[2024-01-24 11:05:44,903] [INFO] DFAST_QC completed!
[2024-01-24 11:05:44,903] [INFO] Total running time: 0h0m41s