[2024-01-24 13:27:58,676] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg109f19ec-9122-4bde-abec-9a322e371aeb/dqc_reference
[2024-01-24 13:27:59,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:59,899] [INFO] Task started: Prodigal
[2024-01-24 13:27:59,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg5048bd72-c2b0-4d94-8862-5bda025c74d3/GCF_014269395.1_ASM1426939v1_genomic.fna.gz | prodigal -d GCF_014269395.1_ASM1426939v1_genomic.fna/cds.fna -a GCF_014269395.1_ASM1426939v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:06,590] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:06,590] [INFO] Task started: HMMsearch
[2024-01-24 13:28:06,591] [INFO] Running command: hmmsearch --tblout GCF_014269395.1_ASM1426939v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg109f19ec-9122-4bde-abec-9a322e371aeb/dqc_reference/reference_markers.hmm GCF_014269395.1_ASM1426939v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:06,817] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:06,818] [INFO] Found 6/6 markers.
[2024-01-24 13:28:06,848] [INFO] Query marker FASTA was written to GCF_014269395.1_ASM1426939v1_genomic.fna/markers.fasta
[2024-01-24 13:28:06,848] [INFO] Task started: Blastn
[2024-01-24 13:28:06,849] [INFO] Running command: blastn -query GCF_014269395.1_ASM1426939v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg109f19ec-9122-4bde-abec-9a322e371aeb/dqc_reference/reference_markers.fasta -out GCF_014269395.1_ASM1426939v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:07,443] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:07,452] [INFO] Selected 16 target genomes.
[2024-01-24 13:28:07,452] [INFO] Target genome list was writen to GCF_014269395.1_ASM1426939v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:07,487] [INFO] Task started: fastANI
[2024-01-24 13:28:07,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg5048bd72-c2b0-4d94-8862-5bda025c74d3/GCF_014269395.1_ASM1426939v1_genomic.fna.gz --refList GCF_014269395.1_ASM1426939v1_genomic.fna/target_genomes.txt --output GCF_014269395.1_ASM1426939v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:15,359] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:15,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg109f19ec-9122-4bde-abec-9a322e371aeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:15,360] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg109f19ec-9122-4bde-abec-9a322e371aeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:15,366] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:15,367] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:15,367] [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
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	78.687	248	860	95	below_threshold
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	78.6826	244	860	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	78.34	216	860	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	78.3191	221	860	95	below_threshold
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	78.1471	203	860	95	below_threshold
'Megasphaera vaginalis' Bordigoni et al. 2020	strain=Marseille-P4857	GCA_900240295.1	2045301	2045301	type	True	77.6862	105	860	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:15,368] [INFO] DFAST Taxonomy check result was written to GCF_014269395.1_ASM1426939v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:15,369] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:15,369] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:15,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg109f19ec-9122-4bde-abec-9a322e371aeb/dqc_reference/checkm_data
[2024-01-24 13:28:15,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:15,398] [INFO] Task started: CheckM
[2024-01-24 13:28:15,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014269395.1_ASM1426939v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014269395.1_ASM1426939v1_genomic.fna/checkm_input GCF_014269395.1_ASM1426939v1_genomic.fna/checkm_result
[2024-01-24 13:28:42,203] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:42,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:42,248] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:42,248] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:42,249] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014269395.1_ASM1426939v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:42,249] [INFO] Task started: Blastn
[2024-01-24 13:28:42,249] [INFO] Running command: blastn -query GCF_014269395.1_ASM1426939v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg109f19ec-9122-4bde-abec-9a322e371aeb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014269395.1_ASM1426939v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:43,085] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:43,090] [INFO] Selected 13 target genomes.
[2024-01-24 13:28:43,090] [INFO] Target genome list was writen to GCF_014269395.1_ASM1426939v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:43,110] [INFO] Task started: fastANI
[2024-01-24 13:28:43,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg5048bd72-c2b0-4d94-8862-5bda025c74d3/GCF_014269395.1_ASM1426939v1_genomic.fna.gz --refList GCF_014269395.1_ASM1426939v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014269395.1_ASM1426939v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:49,450] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:49,460] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:49,460] [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_014269395.1	s__Caecibacter hominis	100.0	854	860	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	99.84	99.81	0.96	0.95	4	conclusive
GCF_003467125.1	s__Caecibacter sp003467125	79.4288	342	860	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	98.80	97.67	0.92	0.89	5	-
GCA_900095875.1	s__Caecibacter massiliensis	79.298	326	860	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	98.76	97.64	0.92	0.86	18	-
GCA_902388315.1	s__Megasphaera sp902388315	79.0224	197	860	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.43	99.12	0.87	0.82	3	-
GCA_900548635.1	s__Megasphaera sp900548635	78.7637	197	860	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.28	98.56	0.89	0.79	3	-
GCF_003010495.1	s__Megasphaera elsdenii	78.7004	243	860	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.27	97.55	0.90	0.81	29	-
GCF_000417505.1	s__Megasphaera sp000417505	78.5797	262	860	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.18	97.65	0.90	0.81	11	-
GCF_003367905.1	s__Megasphaera stantonii	78.312	222	860	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	97.46	96.44	0.91	0.87	8	-
GCA_900752195.1	s__Caecibacter sp900549385	78.2019	180	860	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	99.73	99.52	0.95	0.92	4	-
GCA_900554215.1	s__Megasphaera sp900554215	78.033	168	860	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	95.76	95.76	0.83	0.83	2	-
GCA_900540735.1	s__Megasphaera sp900540735	77.3474	148	860	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.96	99.96	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:49,462] [INFO] GTDB search result was written to GCF_014269395.1_ASM1426939v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:49,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:49,465] [INFO] DFAST_QC result json was written to GCF_014269395.1_ASM1426939v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:49,466] [INFO] DFAST_QC completed!
[2024-01-24 13:28:49,466] [INFO] Total running time: 0h0m51s