[2023-06-05 18:45:13,891] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:45:13,893] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:45:13,893] [INFO] DQC Reference Directory: /var/lib/cwl/stga3aee3f5-a841-44f9-8888-12c0ffcb456b/dqc_reference
[2023-06-05 18:45:14,999] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:45:14,999] [INFO] Task started: Prodigal
[2023-06-05 18:45:14,999] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2074c93-81ad-40f6-b4c9-2c6b2eca2f22/GCA_902836005.1_MGYG-HGUT-05001_genomic.fna.gz | prodigal -d GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/cds.fna -a GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:45:17,583] [INFO] Task succeeded: Prodigal
[2023-06-05 18:45:17,584] [INFO] Task started: HMMsearch
[2023-06-05 18:45:17,584] [INFO] Running command: hmmsearch --tblout GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3aee3f5-a841-44f9-8888-12c0ffcb456b/dqc_reference/reference_markers.hmm GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:45:17,742] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:45:17,743] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb2074c93-81ad-40f6-b4c9-2c6b2eca2f22/GCA_902836005.1_MGYG-HGUT-05001_genomic.fna.gz]
[2023-06-05 18:45:17,758] [INFO] Query marker FASTA was written to GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/markers.fasta
[2023-06-05 18:45:17,758] [INFO] Task started: Blastn
[2023-06-05 18:45:17,758] [INFO] Running command: blastn -query GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/markers.fasta -db /var/lib/cwl/stga3aee3f5-a841-44f9-8888-12c0ffcb456b/dqc_reference/reference_markers.fasta -out GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:45:18,541] [INFO] Task succeeded: Blastn
[2023-06-05 18:45:18,544] [INFO] Selected 6 target genomes.
[2023-06-05 18:45:18,545] [INFO] Target genome list was writen to GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/target_genomes.txt
[2023-06-05 18:45:18,545] [INFO] Task started: fastANI
[2023-06-05 18:45:18,546] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2074c93-81ad-40f6-b4c9-2c6b2eca2f22/GCA_902836005.1_MGYG-HGUT-05001_genomic.fna.gz --refList GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/target_genomes.txt --output GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:45:21,351] [INFO] Task succeeded: fastANI
[2023-06-05 18:45:21,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3aee3f5-a841-44f9-8888-12c0ffcb456b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:45:21,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3aee3f5-a841-44f9-8888-12c0ffcb456b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:45:21,362] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:45:21,362] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:45:21,362] [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
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	88.6939	155	170	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	88.6709	156	170	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	87.6054	153	170	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	86.0547	149	170	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	82.2477	123	170	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	79.2924	61	170	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:45:21,369] [INFO] DFAST Taxonomy check result was written to GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/tc_result.tsv
[2023-06-05 18:45:21,370] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:45:21,370] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:45:21,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3aee3f5-a841-44f9-8888-12c0ffcb456b/dqc_reference/checkm_data
[2023-06-05 18:45:21,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:45:21,397] [INFO] Task started: CheckM
[2023-06-05 18:45:21,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/checkm_input GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/checkm_result
[2023-06-05 18:45:36,997] [INFO] Task succeeded: CheckM
[2023-06-05 18:45:36,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.11%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 18:45:37,093] [INFO] ===== Completeness check finished =====
[2023-06-05 18:45:37,093] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:45:37,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/markers.fasta)
[2023-06-05 18:45:37,094] [INFO] Task started: Blastn
[2023-06-05 18:45:37,094] [INFO] Running command: blastn -query GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/markers.fasta -db /var/lib/cwl/stga3aee3f5-a841-44f9-8888-12c0ffcb456b/dqc_reference/reference_markers_gtdb.fasta -out GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:45:38,440] [INFO] Task succeeded: Blastn
[2023-06-05 18:45:38,444] [INFO] Selected 20 target genomes.
[2023-06-05 18:45:38,444] [INFO] Target genome list was writen to GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:45:38,446] [INFO] Task started: fastANI
[2023-06-05 18:45:38,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2074c93-81ad-40f6-b4c9-2c6b2eca2f22/GCA_902836005.1_MGYG-HGUT-05001_genomic.fna.gz --refList GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/target_genomes_gtdb.txt --output GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:45:46,861] [INFO] Task succeeded: fastANI
[2023-06-05 18:45:46,872] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:45:46,872] [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_003293635.1	s__Faecalibacterium prausnitzii_G	93.8134	156	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.11	95.97	0.86	0.76	34	-
GCA_900758465.1	s__Faecalibacterium sp900758465	93.4844	155	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.14	97.85	0.88	0.87	4	-
GCF_010509575.1	s__Faecalibacterium prausnitzii_C	88.6709	156	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.30	96.44	0.84	0.71	49	-
GCF_002549755.1	s__Faecalibacterium prausnitzii_D	87.2608	152	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.37	96.64	0.86	0.78	38	-
GCF_003287405.1	s__Faecalibacterium prausnitzii_J	87.1279	151	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.32	96.98	0.87	0.83	5	-
GCF_002550015.1	s__Faecalibacterium prausnitzii_A	86.8857	153	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.42	95.34	0.88	0.83	7	-
GCF_002549775.1	s__Faecalibacterium prausnitzii_F	86.7891	149	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.99	97.71	0.95	0.94	3	-
GCA_900539885.1	s__Faecalibacterium sp900539885	86.773	145	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.54	97.23	0.89	0.84	6	-
GCF_002549975.1	s__Faecalibacterium prausnitzii_H	86.6008	153	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.03	97.77	0.90	0.86	9	-
GCF_002550035.1	s__Faecalibacterium prausnitzii_E	86.515	149	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.41	96.74	0.87	0.80	12	-
GCF_003287495.1	s__Faecalibacterium prausnitzii_I	86.3698	154	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.17	97.28	0.90	0.84	9	-
GCA_900539945.1	s__Faecalibacterium sp900539945	86.3581	147	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.71	98.00	0.92	0.86	4	-
GCA_900772565.1	s__Faecalibacterium sp900772565	86.2161	150	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002313795.1	s__Faecalibacterium prausnitzii_L	86.1898	131	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.80	98.80	0.73	0.73	2	-
GCA_900765705.1	s__Faecalibacterium sp900765705	86.0005	130	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.09	97.09	0.66	0.66	2	-
GCA_003449675.1	s__Faecalibacterium sp003449675	85.9395	109	170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	96.56	96.55	0.80	0.74	3	-
--------------------------------------------------------------------------------
[2023-06-05 18:45:46,874] [INFO] GTDB search result was written to GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/result_gtdb.tsv
[2023-06-05 18:45:46,875] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:45:46,877] [INFO] DFAST_QC result json was written to GCA_902836005.1_MGYG-HGUT-05001_genomic.fna/dqc_result.json
[2023-06-05 18:45:46,878] [INFO] DFAST_QC completed!
[2023-06-05 18:45:46,878] [INFO] Total running time: 0h0m33s