[2023-06-29 16:09:02,602] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:09:02,604] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:09:02,604] [INFO] DQC Reference Directory: /var/lib/cwl/stgadf448fe-a60f-4ff8-85d9-2b9fdbc38489/dqc_reference
[2023-06-29 16:09:03,943] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:09:03,944] [INFO] Task started: Prodigal
[2023-06-29 16:09:03,944] [INFO] Running command: gunzip -c /var/lib/cwl/stg8629a093-02ce-42e7-ba7c-7c4d71a95510/GCA_021620585.1_ASM2162058v1_genomic.fna.gz | prodigal -d GCA_021620585.1_ASM2162058v1_genomic.fna/cds.fna -a GCA_021620585.1_ASM2162058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:09:08,885] [INFO] Task succeeded: Prodigal
[2023-06-29 16:09:08,885] [INFO] Task started: HMMsearch
[2023-06-29 16:09:08,885] [INFO] Running command: hmmsearch --tblout GCA_021620585.1_ASM2162058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadf448fe-a60f-4ff8-85d9-2b9fdbc38489/dqc_reference/reference_markers.hmm GCA_021620585.1_ASM2162058v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:09:09,129] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:09:09,130] [INFO] Found 6/6 markers.
[2023-06-29 16:09:09,155] [INFO] Query marker FASTA was written to GCA_021620585.1_ASM2162058v1_genomic.fna/markers.fasta
[2023-06-29 16:09:09,155] [INFO] Task started: Blastn
[2023-06-29 16:09:09,155] [INFO] Running command: blastn -query GCA_021620585.1_ASM2162058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadf448fe-a60f-4ff8-85d9-2b9fdbc38489/dqc_reference/reference_markers.fasta -out GCA_021620585.1_ASM2162058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:09:09,822] [INFO] Task succeeded: Blastn
[2023-06-29 16:09:09,827] [INFO] Selected 31 target genomes.
[2023-06-29 16:09:09,828] [INFO] Target genome list was writen to GCA_021620585.1_ASM2162058v1_genomic.fna/target_genomes.txt
[2023-06-29 16:09:09,829] [INFO] Task started: fastANI
[2023-06-29 16:09:09,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg8629a093-02ce-42e7-ba7c-7c4d71a95510/GCA_021620585.1_ASM2162058v1_genomic.fna.gz --refList GCA_021620585.1_ASM2162058v1_genomic.fna/target_genomes.txt --output GCA_021620585.1_ASM2162058v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:09:30,141] [INFO] Task succeeded: fastANI
[2023-06-29 16:09:30,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadf448fe-a60f-4ff8-85d9-2b9fdbc38489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:09:30,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadf448fe-a60f-4ff8-85d9-2b9fdbc38489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:09:30,150] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:09:30,151] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:09:30,151] [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
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.9535	73	546	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.9142	68	546	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.7404	67	546	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:09:30,153] [INFO] DFAST Taxonomy check result was written to GCA_021620585.1_ASM2162058v1_genomic.fna/tc_result.tsv
[2023-06-29 16:09:30,154] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:09:30,154] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:09:30,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadf448fe-a60f-4ff8-85d9-2b9fdbc38489/dqc_reference/checkm_data
[2023-06-29 16:09:30,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:09:30,183] [INFO] Task started: CheckM
[2023-06-29 16:09:30,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021620585.1_ASM2162058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021620585.1_ASM2162058v1_genomic.fna/checkm_input GCA_021620585.1_ASM2162058v1_genomic.fna/checkm_result
[2023-06-29 16:09:51,868] [INFO] Task succeeded: CheckM
[2023-06-29 16:09:51,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:09:51,891] [INFO] ===== Completeness check finished =====
[2023-06-29 16:09:51,891] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:09:51,892] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021620585.1_ASM2162058v1_genomic.fna/markers.fasta)
[2023-06-29 16:09:51,892] [INFO] Task started: Blastn
[2023-06-29 16:09:51,892] [INFO] Running command: blastn -query GCA_021620585.1_ASM2162058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadf448fe-a60f-4ff8-85d9-2b9fdbc38489/dqc_reference/reference_markers_gtdb.fasta -out GCA_021620585.1_ASM2162058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:09:52,990] [INFO] Task succeeded: Blastn
[2023-06-29 16:09:52,995] [INFO] Selected 19 target genomes.
[2023-06-29 16:09:52,995] [INFO] Target genome list was writen to GCA_021620585.1_ASM2162058v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:09:52,998] [INFO] Task started: fastANI
[2023-06-29 16:09:52,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg8629a093-02ce-42e7-ba7c-7c4d71a95510/GCA_021620585.1_ASM2162058v1_genomic.fna.gz --refList GCA_021620585.1_ASM2162058v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021620585.1_ASM2162058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:10:04,127] [INFO] Task succeeded: fastANI
[2023-06-29 16:10:04,145] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:10:04,145] [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
GCA_000434615.1	s__CAG-510 sp000434615	98.5176	506	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	98.10	97.86	0.88	0.86	6	conclusive
GCA_002432425.1	s__CAG-510 sp002432425	93.3014	481	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	97.90	96.14	0.90	0.83	7	-
GCA_900551115.1	s__CAG-510 sp900551115	78.2432	157	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017482205.1	s__CAG-510 sp017482205	78.1421	118	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	98.99	98.99	0.84	0.84	2	-
GCA_900550475.1	s__CAG-510 sp900550475	77.7879	133	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	99.15	99.15	0.91	0.91	2	-
GCA_910577105.1	s__CAG-510 sp910577105	77.5812	91	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003584705.1	s__Acetatifactor sp900066565	77.5484	108	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.01	97.56	0.88	0.80	26	-
GCA_910577015.1	s__CAG-510 sp910577015	77.3413	107	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465845.1	s__Acetatifactor sp017465845	77.0387	59	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554205.1	s__Acetatifactor sp900554205	77.0233	73	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.93	99.93	0.88	0.88	2	-
GCA_016303085.1	s__Acetatifactor sp016303085	76.743	62	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803415.1	s__CAG-95 sp014803415	76.7017	56	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	97.80	97.80	0.82	0.82	2	-
GCA_910577035.1	s__Acetatifactor sp910577035	76.618	52	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003481005.1	s__Eisenbergiella sp900066775	76.3994	59	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	97.95	96.96	0.88	0.78	15	-
GCA_900542015.1	s__UBA2882 sp900542015	76.2793	50	546	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	99.84	99.68	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-29 16:10:04,147] [INFO] GTDB search result was written to GCA_021620585.1_ASM2162058v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:10:04,148] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:10:04,179] [INFO] DFAST_QC result json was written to GCA_021620585.1_ASM2162058v1_genomic.fna/dqc_result.json
[2023-06-29 16:10:04,180] [INFO] DFAST_QC completed!
[2023-06-29 16:10:04,180] [INFO] Total running time: 0h1m2s