[2023-06-28 19:48:05,715] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:48:05,717] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:48:05,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d1f20e3-86c6-45b2-860a-6dce7b772c82/dqc_reference
[2023-06-28 19:48:08,330] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:48:08,331] [INFO] Task started: Prodigal
[2023-06-28 19:48:08,331] [INFO] Running command: gunzip -c /var/lib/cwl/stge6633ffe-5b64-4731-a161-bcb7d717a2cb/GCA_944321175.1_E16_bin154_genomic.fna.gz | prodigal -d GCA_944321175.1_E16_bin154_genomic.fna/cds.fna -a GCA_944321175.1_E16_bin154_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:48:22,473] [INFO] Task succeeded: Prodigal
[2023-06-28 19:48:22,473] [INFO] Task started: HMMsearch
[2023-06-28 19:48:22,474] [INFO] Running command: hmmsearch --tblout GCA_944321175.1_E16_bin154_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d1f20e3-86c6-45b2-860a-6dce7b772c82/dqc_reference/reference_markers.hmm GCA_944321175.1_E16_bin154_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:48:22,764] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:48:22,765] [INFO] Found 6/6 markers.
[2023-06-28 19:48:22,787] [INFO] Query marker FASTA was written to GCA_944321175.1_E16_bin154_genomic.fna/markers.fasta
[2023-06-28 19:48:22,788] [INFO] Task started: Blastn
[2023-06-28 19:48:22,788] [INFO] Running command: blastn -query GCA_944321175.1_E16_bin154_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d1f20e3-86c6-45b2-860a-6dce7b772c82/dqc_reference/reference_markers.fasta -out GCA_944321175.1_E16_bin154_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:23,465] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:23,473] [INFO] Selected 22 target genomes.
[2023-06-28 19:48:23,473] [INFO] Target genome list was writen to GCA_944321175.1_E16_bin154_genomic.fna/target_genomes.txt
[2023-06-28 19:48:23,482] [INFO] Task started: fastANI
[2023-06-28 19:48:23,482] [INFO] Running command: fastANI --query /var/lib/cwl/stge6633ffe-5b64-4731-a161-bcb7d717a2cb/GCA_944321175.1_E16_bin154_genomic.fna.gz --refList GCA_944321175.1_E16_bin154_genomic.fna/target_genomes.txt --output GCA_944321175.1_E16_bin154_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:48:35,345] [INFO] Task succeeded: fastANI
[2023-06-28 19:48:35,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d1f20e3-86c6-45b2-860a-6dce7b772c82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:48:35,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d1f20e3-86c6-45b2-860a-6dce7b772c82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:48:35,361] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:48:35,361] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:48:35,361] [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
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	80.7939	499	767	95	below_threshold
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	78.7359	265	767	95	below_threshold
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	78.7087	242	767	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	78.3204	268	767	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	78.2773	271	767	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	78.2731	270	767	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	78.2725	240	767	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	78.1983	262	767	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	78.1848	247	767	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	78.1353	247	767	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	78.1145	241	767	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	77.948	248	767	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	77.8903	220	767	95	below_threshold
Alistipes putredinis	strain=DSM 17216	GCA_000154465.1	28117	28117	type	True	77.8266	187	767	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	77.7024	233	767	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	76.658	89	767	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_000321205.1	1470347	1470347	type	True	76.6406	88	767	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:48:35,364] [INFO] DFAST Taxonomy check result was written to GCA_944321175.1_E16_bin154_genomic.fna/tc_result.tsv
[2023-06-28 19:48:35,364] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:48:35,364] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:48:35,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d1f20e3-86c6-45b2-860a-6dce7b772c82/dqc_reference/checkm_data
[2023-06-28 19:48:35,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:48:35,401] [INFO] Task started: CheckM
[2023-06-28 19:48:35,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944321175.1_E16_bin154_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944321175.1_E16_bin154_genomic.fna/checkm_input GCA_944321175.1_E16_bin154_genomic.fna/checkm_result
[2023-06-28 19:49:17,634] [INFO] Task succeeded: CheckM
[2023-06-28 19:49:17,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:49:17,655] [INFO] ===== Completeness check finished =====
[2023-06-28 19:49:17,656] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:49:17,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944321175.1_E16_bin154_genomic.fna/markers.fasta)
[2023-06-28 19:49:17,656] [INFO] Task started: Blastn
[2023-06-28 19:49:17,656] [INFO] Running command: blastn -query GCA_944321175.1_E16_bin154_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d1f20e3-86c6-45b2-860a-6dce7b772c82/dqc_reference/reference_markers_gtdb.fasta -out GCA_944321175.1_E16_bin154_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:49:18,558] [INFO] Task succeeded: Blastn
[2023-06-28 19:49:18,563] [INFO] Selected 22 target genomes.
[2023-06-28 19:49:18,563] [INFO] Target genome list was writen to GCA_944321175.1_E16_bin154_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:49:18,569] [INFO] Task started: fastANI
[2023-06-28 19:49:18,569] [INFO] Running command: fastANI --query /var/lib/cwl/stge6633ffe-5b64-4731-a161-bcb7d717a2cb/GCA_944321175.1_E16_bin154_genomic.fna.gz --refList GCA_944321175.1_E16_bin154_genomic.fna/target_genomes_gtdb.txt --output GCA_944321175.1_E16_bin154_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:49:28,985] [INFO] Task succeeded: fastANI
[2023-06-28 19:49:29,002] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 19:49:29,003] [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_006542665.1	s__Alistipes communis	80.7859	500	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.74	98.62	0.92	0.87	10	-
GCA_900552955.1	s__Alistipes sp900552955	80.5467	309	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214725.1	s__Alistipes sp905214725	80.2839	411	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550375.1	s__Alistipes sp900550375	79.9607	405	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900604385.1	s__Alistipes megaguti	78.7359	265	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.62	97.58	0.76	0.76	3	-
GCA_900544265.1	s__Alistipes merdavium	78.7149	239	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.60	98.07	0.91	0.88	5	-
GCF_006542685.1	s__Alistipes dispar	78.7087	242	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.96	0.94	0.89	7	-
GCA_900542505.1	s__Alistipes stercorigallinarum	78.3607	213	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCA_019118605.1	s__Alistipes faecavium	78.3057	213	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541585.1	s__Alistipes sp900541585	78.1896	219	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCA_019115745.1	s__Alistipes intestinigallinarum	78.1886	224	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265365.1	s__Alistipes finegoldii	78.185	263	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	-
GCA_900553175.1	s__Alistipes sp900553175	78.1442	169	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001941065.1	s__Alistipes sp001941065	78.0974	220	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107675.1	s__Alistipes timonensis	77.8903	220	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.44	0.92	0.87	7	-
GCF_000154465.1	s__Alistipes putredinis	77.8266	187	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.94	97.62	0.91	0.76	28	-
GCA_019113885.1	s__Alistipes intestinipullorum	77.8236	191	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059845.1	s__Alistipes sp015059845	76.5331	51	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.42	97.01	0.88	0.86	7	-
--------------------------------------------------------------------------------
[2023-06-28 19:49:29,005] [INFO] GTDB search result was written to GCA_944321175.1_E16_bin154_genomic.fna/result_gtdb.tsv
[2023-06-28 19:49:29,005] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:49:29,010] [INFO] DFAST_QC result json was written to GCA_944321175.1_E16_bin154_genomic.fna/dqc_result.json
[2023-06-28 19:49:29,010] [INFO] DFAST_QC completed!
[2023-06-28 19:49:29,010] [INFO] Total running time: 0h1m23s