[2023-06-05 18:02:55,367] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:02:55,381] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:02:55,381] [INFO] DQC Reference Directory: /var/lib/cwl/stg9cdc4fdd-a255-4bcd-b5b0-3082d68fba83/dqc_reference
[2023-06-05 18:02:56,593] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:02:56,594] [INFO] Task started: Prodigal
[2023-06-05 18:02:56,594] [INFO] Running command: gunzip -c /var/lib/cwl/stg269a528b-f89e-4def-aa9c-abcd571b1ead/GCA_902836775.1_MGYG-HGUT-04883_genomic.fna.gz | prodigal -d GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/cds.fna -a GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:02:59,826] [INFO] Task succeeded: Prodigal
[2023-06-05 18:02:59,826] [INFO] Task started: HMMsearch
[2023-06-05 18:02:59,826] [INFO] Running command: hmmsearch --tblout GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9cdc4fdd-a255-4bcd-b5b0-3082d68fba83/dqc_reference/reference_markers.hmm GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:02:59,969] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:02:59,970] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg269a528b-f89e-4def-aa9c-abcd571b1ead/GCA_902836775.1_MGYG-HGUT-04883_genomic.fna.gz]
[2023-06-05 18:03:00,264] [INFO] Query marker FASTA was written to GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/markers.fasta
[2023-06-05 18:03:00,264] [INFO] Task started: Blastn
[2023-06-05 18:03:00,264] [INFO] Running command: blastn -query GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cdc4fdd-a255-4bcd-b5b0-3082d68fba83/dqc_reference/reference_markers.fasta -out GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:03:00,911] [INFO] Task succeeded: Blastn
[2023-06-05 18:03:00,926] [INFO] Selected 15 target genomes.
[2023-06-05 18:03:00,926] [INFO] Target genome list was writen to GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/target_genomes.txt
[2023-06-05 18:03:00,940] [INFO] Task started: fastANI
[2023-06-05 18:03:00,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg269a528b-f89e-4def-aa9c-abcd571b1ead/GCA_902836775.1_MGYG-HGUT-04883_genomic.fna.gz --refList GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/target_genomes.txt --output GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:03:07,977] [INFO] Task succeeded: fastANI
[2023-06-05 18:03:07,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9cdc4fdd-a255-4bcd-b5b0-3082d68fba83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:03:07,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9cdc4fdd-a255-4bcd-b5b0-3082d68fba83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:03:07,984] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:03:07,984] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:03:07,984] [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
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	93.6614	136	148	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	93.5967	137	148	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	93.5949	136	148	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	82.2113	55	148	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.117	54	148	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	78.5404	51	148	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:03:08,096] [INFO] DFAST Taxonomy check result was written to GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/tc_result.tsv
[2023-06-05 18:03:08,097] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:03:08,097] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:03:08,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9cdc4fdd-a255-4bcd-b5b0-3082d68fba83/dqc_reference/checkm_data
[2023-06-05 18:03:08,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:03:08,118] [INFO] Task started: CheckM
[2023-06-05 18:03:08,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/checkm_input GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/checkm_result
[2023-06-05 18:03:23,407] [INFO] Task succeeded: CheckM
[2023-06-05 18:03:23,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:03:23,432] [INFO] ===== Completeness check finished =====
[2023-06-05 18:03:23,432] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:03:23,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/markers.fasta)
[2023-06-05 18:03:23,432] [INFO] Task started: Blastn
[2023-06-05 18:03:23,432] [INFO] Running command: blastn -query GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cdc4fdd-a255-4bcd-b5b0-3082d68fba83/dqc_reference/reference_markers_gtdb.fasta -out GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:03:24,618] [INFO] Task succeeded: Blastn
[2023-06-05 18:03:24,622] [INFO] Selected 38 target genomes.
[2023-06-05 18:03:24,622] [INFO] Target genome list was writen to GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:03:24,748] [INFO] Task started: fastANI
[2023-06-05 18:03:24,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg269a528b-f89e-4def-aa9c-abcd571b1ead/GCA_902836775.1_MGYG-HGUT-04883_genomic.fna.gz --refList GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/target_genomes_gtdb.txt --output GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:03:35,499] [INFO] Task succeeded: fastANI
[2023-06-05 18:03:35,517] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:03:35,518] [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_900754525.1	s__Collinsella sp900754525	93.8856	129	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0709	95.23	95.09	0.81	0.78	4	-
GCA_900541245.1	s__Collinsella sp900541245	93.815	132	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.072	100.00	100.00	1.00	1.00	2	-
GCA_905209455.1	s__Collinsella sp905209455	93.6463	128	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1399	99.94	99.94	0.95	0.95	2	-
GCA_900758885.1	s__Collinsella sp900758885	93.645	128	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0066	N/A	N/A	N/A	N/A	1	-
GCA_900541175.1	s__Collinsella sp900541175	93.6374	134	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2242	N/A	N/A	N/A	N/A	1	-
GCA_900541875.1	s__Collinsella sp900541875	93.6116	131	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.60	95.21	0.93	0.87	3	-
GCF_010509075.1	s__Collinsella aerofaciens	93.5967	137	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.99	99.98	1.00	0.99	4	-
GCA_900544865.1	s__Collinsella sp900544865	93.5676	134	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018380015.1	s__Collinsella sp018380015	93.5651	134	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1883	96.09	95.27	0.89	0.86	8	-
GCA_900547765.1	s__Collinsella sp900547765	93.5266	130	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541205.1	s__Collinsella sp900541205	93.4938	136	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.97	99.97	0.98	0.98	2	-
GCA_905216145.1	s__Collinsella sp905216145	93.4801	139	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550195.1	s__Collinsella sp900550195	93.3402	136	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1628	N/A	N/A	N/A	N/A	1	-
GCA_900551975.1	s__Collinsella sp900551975	93.3335	125	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541235.1	s__Collinsella sp900541235	93.1735	137	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.02	95.02	0.86	0.86	2	-
GCF_003438495.1	s__Collinsella sp003438495	93.1503	135	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003439125.1	s__Collinsella sp003439125	93.1499	136	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.74	95.07	0.88	0.85	15	-
GCF_015670745.1	s__Collinsella aerofaciens_T	93.1078	139	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0363	95.05	95.05	0.90	0.90	2	-
GCA_900550185.1	s__Collinsella sp900550185	93.1002	123	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214435.1	s__Collinsella sp905214435	93.0783	131	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.174	95.31	95.19	0.87	0.85	5	-
GCA_905215385.1	s__Collinsella sp905215385	93.0464	138	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2035	95.42	95.23	0.87	0.82	17	-
GCA_900544875.1	s__Collinsella sp900544875	92.9661	134	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542325.1	s__Collinsella sp900542325	92.9245	130	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900757465.1	s__Collinsella sp900757465	92.9096	126	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757595.1	s__Collinsella sp900757595	92.8648	124	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549345.1	s__Collinsella sp900549345	92.6079	128	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003436275.1	s__Collinsella sp003436275	92.5404	138	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.89	95.08	0.88	0.83	16	-
GCA_900540875.1	s__Collinsella sp900540875	92.5295	135	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.98	0.98	2	-
GCA_900549185.1	s__Collinsella sp900549185	92.4636	133	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551205.1	s__Collinsella sp900551205	92.3988	123	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.45	95.34	0.91	0.90	4	-
GCA_900546085.1	s__Collinsella sp900546085	92.3726	118	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0166	N/A	N/A	N/A	N/A	1	-
GCA_900550835.1	s__Collinsella sp900550835	92.3492	126	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.40	95.47	0.90	0.85	4	-
GCA_900757285.1	s__Collinsella sp900757285	91.9824	115	148	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:03:35,520] [INFO] GTDB search result was written to GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/result_gtdb.tsv
[2023-06-05 18:03:35,520] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:03:35,526] [INFO] DFAST_QC result json was written to GCA_902836775.1_MGYG-HGUT-04883_genomic.fna/dqc_result.json
[2023-06-05 18:03:35,526] [INFO] DFAST_QC completed!
[2023-06-05 18:03:35,527] [INFO] Total running time: 0h0m40s