[2023-06-16 19:33:13,888] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:33:13,890] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:33:13,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg57988f9c-88a7-49cc-8631-85a50f668a3f/dqc_reference
[2023-06-16 19:33:15,013] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:33:15,014] [INFO] Task started: Prodigal
[2023-06-16 19:33:15,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg606b5333-4f1c-4f87-8bd1-88592fcf879a/GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna.gz | prodigal -d GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/cds.fna -a GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:33:20,343] [INFO] Task succeeded: Prodigal
[2023-06-16 19:33:20,343] [INFO] Task started: HMMsearch
[2023-06-16 19:33:20,343] [INFO] Running command: hmmsearch --tblout GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57988f9c-88a7-49cc-8631-85a50f668a3f/dqc_reference/reference_markers.hmm GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:33:20,544] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:33:20,552] [INFO] Found 6/6 markers.
[2023-06-16 19:33:20,575] [INFO] Query marker FASTA was written to GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/markers.fasta
[2023-06-16 19:33:20,575] [INFO] Task started: Blastn
[2023-06-16 19:33:20,575] [INFO] Running command: blastn -query GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/markers.fasta -db /var/lib/cwl/stg57988f9c-88a7-49cc-8631-85a50f668a3f/dqc_reference/reference_markers.fasta -out GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:33:21,132] [INFO] Task succeeded: Blastn
[2023-06-16 19:33:21,135] [INFO] Selected 9 target genomes.
[2023-06-16 19:33:21,136] [INFO] Target genome list was writen to GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/target_genomes.txt
[2023-06-16 19:33:21,137] [INFO] Task started: fastANI
[2023-06-16 19:33:21,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg606b5333-4f1c-4f87-8bd1-88592fcf879a/GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna.gz --refList GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/target_genomes.txt --output GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:33:27,550] [INFO] Task succeeded: fastANI
[2023-06-16 19:33:27,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57988f9c-88a7-49cc-8631-85a50f668a3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:33:27,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57988f9c-88a7-49cc-8631-85a50f668a3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:33:27,557] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-06-16 19:33:27,557] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-16 19:33:27,557] [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 massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	99.9327	772	776	95	conclusive
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	82.3842	479	776	95	below_threshold
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	82.2792	484	776	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	78.7581	279	776	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	78.6847	288	776	95	below_threshold
'Megasphaera vaginalis' Bordigoni et al. 2020	strain=Marseille-P4857	GCA_900240295.1	2045301	2045301	type	True	77.573	118	776	95	below_threshold
Colibacter massiliensis	strain=Marseille-P2911	GCA_900095855.1	1852379	1852379	type	True	77.339	92	776	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:33:27,564] [INFO] DFAST Taxonomy check result was written to GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/tc_result.tsv
[2023-06-16 19:33:27,564] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:33:27,564] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:33:27,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57988f9c-88a7-49cc-8631-85a50f668a3f/dqc_reference/checkm_data
[2023-06-16 19:33:27,565] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:33:27,592] [INFO] Task started: CheckM
[2023-06-16 19:33:27,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/checkm_input GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/checkm_result
[2023-06-16 19:33:48,282] [INFO] Task succeeded: CheckM
[2023-06-16 19:33:48,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:33:48,300] [INFO] ===== Completeness check finished =====
[2023-06-16 19:33:48,301] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:33:48,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/markers.fasta)
[2023-06-16 19:33:48,302] [INFO] Task started: Blastn
[2023-06-16 19:33:48,302] [INFO] Running command: blastn -query GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/markers.fasta -db /var/lib/cwl/stg57988f9c-88a7-49cc-8631-85a50f668a3f/dqc_reference/reference_markers_gtdb.fasta -out GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:33:49,131] [INFO] Task succeeded: Blastn
[2023-06-16 19:33:49,134] [INFO] Selected 7 target genomes.
[2023-06-16 19:33:49,134] [INFO] Target genome list was writen to GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:33:49,135] [INFO] Task started: fastANI
[2023-06-16 19:33:49,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg606b5333-4f1c-4f87-8bd1-88592fcf879a/GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna.gz --refList GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/target_genomes_gtdb.txt --output GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:33:53,048] [INFO] Task succeeded: fastANI
[2023-06-16 19:33:53,054] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:33:53,054] [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_000455225.1	s__Megasphaera massiliensis	99.9327	772	776	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.41	96.06	0.94	0.88	8	conclusive
GCA_002319965.1	s__Megasphaera sp002319965	94.0414	567	776	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.41	98.03	0.89	0.89	4	-
GCA_900539295.1	s__Megasphaera sp900539295	90.265	620	776	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001546855.1	s__Megasphaera sp001546855	89.8648	640	776	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.96	99.94	0.97	0.94	9	-
GCF_000417505.1	s__Megasphaera sp000417505	82.2866	491	776	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.18	97.65	0.90	0.81	11	-
GCA_902388315.1	s__Megasphaera sp902388315	82.2858	347	776	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	81.9417	358	776	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.28	98.56	0.89	0.79	3	-
--------------------------------------------------------------------------------
[2023-06-16 19:33:53,056] [INFO] GTDB search result was written to GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/result_gtdb.tsv
[2023-06-16 19:33:53,057] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:33:53,059] [INFO] DFAST_QC result json was written to GCA_905211455.1_ERR414446-mag-bin.2_genomic.fna/dqc_result.json
[2023-06-16 19:33:53,059] [INFO] DFAST_QC completed!
[2023-06-16 19:33:53,059] [INFO] Total running time: 0h0m39s