[2024-01-24 14:03:02,869] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:02,871] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:02,871] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fe6a386-4767-4e08-8438-efcecb808ab7/dqc_reference
[2024-01-24 14:03:04,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:04,153] [INFO] Task started: Prodigal
[2024-01-24 14:03:04,153] [INFO] Running command: gunzip -c /var/lib/cwl/stg5715d8cc-68b2-4301-8e2a-8c9357fedbc9/GCF_000350165.1_ASM35016v1_genomic.fna.gz | prodigal -d GCF_000350165.1_ASM35016v1_genomic.fna/cds.fna -a GCF_000350165.1_ASM35016v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:08,656] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:08,657] [INFO] Task started: HMMsearch
[2024-01-24 14:03:08,657] [INFO] Running command: hmmsearch --tblout GCF_000350165.1_ASM35016v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fe6a386-4767-4e08-8438-efcecb808ab7/dqc_reference/reference_markers.hmm GCF_000350165.1_ASM35016v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:08,968] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:08,969] [INFO] Found 6/6 markers.
[2024-01-24 14:03:09,012] [INFO] Query marker FASTA was written to GCF_000350165.1_ASM35016v1_genomic.fna/markers.fasta
[2024-01-24 14:03:09,012] [INFO] Task started: Blastn
[2024-01-24 14:03:09,013] [INFO] Running command: blastn -query GCF_000350165.1_ASM35016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fe6a386-4767-4e08-8438-efcecb808ab7/dqc_reference/reference_markers.fasta -out GCF_000350165.1_ASM35016v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:09,777] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:09,781] [INFO] Selected 14 target genomes.
[2024-01-24 14:03:09,782] [INFO] Target genome list was writen to GCF_000350165.1_ASM35016v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:09,912] [INFO] Task started: fastANI
[2024-01-24 14:03:09,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg5715d8cc-68b2-4301-8e2a-8c9357fedbc9/GCF_000350165.1_ASM35016v1_genomic.fna.gz --refList GCF_000350165.1_ASM35016v1_genomic.fna/target_genomes.txt --output GCF_000350165.1_ASM35016v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:18,727] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:18,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fe6a386-4767-4e08-8438-efcecb808ab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:18,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fe6a386-4767-4e08-8438-efcecb808ab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:18,735] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:18,735] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:18,735] [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
Halanaerobium saccharolyticum subsp. saccharolyticum	strain=type strain:DSM 6643	GCA_000350165.1	267736	43595	type	True	100.0	946	947	95	conclusive
Halanaerobium congolense	strain=DSMZ 11287	GCA_004366375.1	54121	54121	type	True	82.7885	602	947	95	below_threshold
Halanaerobium praevalens	strain=DSM 2228	GCA_000165465.1	2331	2331	type	True	80.717	428	947	95	below_threshold
Halanaerobium kushneri	strain=ATCC 700103	GCA_900156285.1	56779	56779	type	True	80.6739	498	947	95	below_threshold
Halanaerobium salsuginis	strain=ATCC 51327	GCA_900114545.1	29563	29563	type	True	78.8796	285	947	95	below_threshold
Orenia marismortui	strain=DSM 5156	GCA_000379025.1	46469	46469	type	True	75.681	65	947	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:18,737] [INFO] DFAST Taxonomy check result was written to GCF_000350165.1_ASM35016v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:18,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:18,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:18,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fe6a386-4767-4e08-8438-efcecb808ab7/dqc_reference/checkm_data
[2024-01-24 14:03:18,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:18,774] [INFO] Task started: CheckM
[2024-01-24 14:03:18,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000350165.1_ASM35016v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000350165.1_ASM35016v1_genomic.fna/checkm_input GCF_000350165.1_ASM35016v1_genomic.fna/checkm_result
[2024-01-24 14:03:40,614] [INFO] Task succeeded: CheckM
[2024-01-24 14:03:40,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:03:40,637] [INFO] ===== Completeness check finished =====
[2024-01-24 14:03:40,638] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:03:40,638] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000350165.1_ASM35016v1_genomic.fna/markers.fasta)
[2024-01-24 14:03:40,639] [INFO] Task started: Blastn
[2024-01-24 14:03:40,639] [INFO] Running command: blastn -query GCF_000350165.1_ASM35016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fe6a386-4767-4e08-8438-efcecb808ab7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000350165.1_ASM35016v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:41,704] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:41,707] [INFO] Selected 8 target genomes.
[2024-01-24 14:03:41,707] [INFO] Target genome list was writen to GCF_000350165.1_ASM35016v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:03:41,717] [INFO] Task started: fastANI
[2024-01-24 14:03:41,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg5715d8cc-68b2-4301-8e2a-8c9357fedbc9/GCF_000350165.1_ASM35016v1_genomic.fna.gz --refList GCF_000350165.1_ASM35016v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000350165.1_ASM35016v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:03:47,250] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:47,258] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:03:47,258] [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_000350165.1	s__Halanaerobium saccharolyticum	100.0	946	947	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004366375.1	s__Halanaerobium congolense	82.7975	601	947	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	97.80	95.58	0.84	0.73	19	-
GCF_003053565.1	s__Halanaerobium saccharolyticum_B	81.4776	502	947	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	96.03	96.03	0.86	0.86	2	-
GCF_003259895.1	s__Halanaerobium saccharolyticum_A	81.3706	544	947	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	100.00	99.99	0.99	0.99	3	-
GCF_004362045.1	s__Halanaerobium saccharolyticum_C	81.1272	545	947	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003070825.1	s__Halanaerobium sp003070825	81.0322	368	947	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165465.1	s__Halanaerobium praevalens	80.7221	426	947	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156285.1	s__Halanaerobium kushneri	80.6721	500	947	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	97.73	97.73	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:03:47,260] [INFO] GTDB search result was written to GCF_000350165.1_ASM35016v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:03:47,260] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:03:47,263] [INFO] DFAST_QC result json was written to GCF_000350165.1_ASM35016v1_genomic.fna/dqc_result.json
[2024-01-24 14:03:47,264] [INFO] DFAST_QC completed!
[2024-01-24 14:03:47,264] [INFO] Total running time: 0h0m44s