[2024-01-24 14:05:16,268] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:16,269] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:16,270] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b52eb03-4174-465f-b5ad-c1c36644b221/dqc_reference
[2024-01-24 14:05:17,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:17,506] [INFO] Task started: Prodigal
[2024-01-24 14:05:17,506] [INFO] Running command: gunzip -c /var/lib/cwl/stgec684507-880f-46d7-a668-e13527f39506/GCF_004366375.1_ASM436637v1_genomic.fna.gz | prodigal -d GCF_004366375.1_ASM436637v1_genomic.fna/cds.fna -a GCF_004366375.1_ASM436637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:21,742] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:21,742] [INFO] Task started: HMMsearch
[2024-01-24 14:05:21,743] [INFO] Running command: hmmsearch --tblout GCF_004366375.1_ASM436637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b52eb03-4174-465f-b5ad-c1c36644b221/dqc_reference/reference_markers.hmm GCF_004366375.1_ASM436637v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:22,039] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:22,041] [INFO] Found 6/6 markers.
[2024-01-24 14:05:22,072] [INFO] Query marker FASTA was written to GCF_004366375.1_ASM436637v1_genomic.fna/markers.fasta
[2024-01-24 14:05:22,072] [INFO] Task started: Blastn
[2024-01-24 14:05:22,072] [INFO] Running command: blastn -query GCF_004366375.1_ASM436637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b52eb03-4174-465f-b5ad-c1c36644b221/dqc_reference/reference_markers.fasta -out GCF_004366375.1_ASM436637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:22,794] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:22,798] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:22,798] [INFO] Target genome list was writen to GCF_004366375.1_ASM436637v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:22,814] [INFO] Task started: fastANI
[2024-01-24 14:05:22,814] [INFO] Running command: fastANI --query /var/lib/cwl/stgec684507-880f-46d7-a668-e13527f39506/GCF_004366375.1_ASM436637v1_genomic.fna.gz --refList GCF_004366375.1_ASM436637v1_genomic.fna/target_genomes.txt --output GCF_004366375.1_ASM436637v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:29,829] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:29,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b52eb03-4174-465f-b5ad-c1c36644b221/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:29,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b52eb03-4174-465f-b5ad-c1c36644b221/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:29,840] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:29,841] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:29,841] [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 congolense	strain=DSMZ 11287	GCA_004366375.1	54121	54121	type	True	100.0	895	897	95	conclusive
Halanaerobium saccharolyticum subsp. saccharolyticum	strain=type strain:DSM 6643	GCA_000350165.1	267736	43595	type	True	82.9528	612	897	95	below_threshold
Halanaerobium kushneri	strain=ATCC 700103	GCA_900156285.1	56779	56779	type	True	81.4603	483	897	95	below_threshold
Halanaerobium praevalens	strain=DSM 2228	GCA_000165465.1	2331	2331	type	True	80.4671	382	897	95	below_threshold
Halanaerobium salsuginis	strain=ATCC 51327	GCA_900114545.1	29563	29563	type	True	78.7697	285	897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:29,843] [INFO] DFAST Taxonomy check result was written to GCF_004366375.1_ASM436637v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:29,843] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:29,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:29,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b52eb03-4174-465f-b5ad-c1c36644b221/dqc_reference/checkm_data
[2024-01-24 14:05:29,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:29,877] [INFO] Task started: CheckM
[2024-01-24 14:05:29,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004366375.1_ASM436637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004366375.1_ASM436637v1_genomic.fna/checkm_input GCF_004366375.1_ASM436637v1_genomic.fna/checkm_result
[2024-01-24 14:05:50,704] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:50,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:50,724] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:50,725] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:50,725] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004366375.1_ASM436637v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:50,726] [INFO] Task started: Blastn
[2024-01-24 14:05:50,726] [INFO] Running command: blastn -query GCF_004366375.1_ASM436637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b52eb03-4174-465f-b5ad-c1c36644b221/dqc_reference/reference_markers_gtdb.fasta -out GCF_004366375.1_ASM436637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:51,799] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:51,802] [INFO] Selected 9 target genomes.
[2024-01-24 14:05:51,802] [INFO] Target genome list was writen to GCF_004366375.1_ASM436637v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:51,811] [INFO] Task started: fastANI
[2024-01-24 14:05:51,812] [INFO] Running command: fastANI --query /var/lib/cwl/stgec684507-880f-46d7-a668-e13527f39506/GCF_004366375.1_ASM436637v1_genomic.fna.gz --refList GCF_004366375.1_ASM436637v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004366375.1_ASM436637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:57,402] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:57,410] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:57,411] [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_004366375.1	s__Halanaerobium congolense	100.0	895	897	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	97.80	95.58	0.84	0.73	19	conclusive
GCF_000350165.1	s__Halanaerobium saccharolyticum	82.9693	611	897	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_004362045.1	s__Halanaerobium saccharolyticum_C	82.4811	528	897	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_003053565.1	s__Halanaerobium saccharolyticum_B	82.3882	512	897	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	82.2498	551	897	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	100.00	99.99	0.99	0.99	3	-
GCA_003070825.1	s__Halanaerobium sp003070825	82.0722	355	897	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	81.4624	482	897	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	97.73	97.73	0.83	0.83	2	-
GCF_000165465.1	s__Halanaerobium praevalens	80.4354	385	897	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:05:57,413] [INFO] GTDB search result was written to GCF_004366375.1_ASM436637v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:57,413] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:57,417] [INFO] DFAST_QC result json was written to GCF_004366375.1_ASM436637v1_genomic.fna/dqc_result.json
[2024-01-24 14:05:57,417] [INFO] DFAST_QC completed!
[2024-01-24 14:05:57,418] [INFO] Total running time: 0h0m41s