[2023-06-05 02:37:18,087] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:37:18,089] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:37:18,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e10c052-c889-4f1d-8c7f-3ac8a1854df3/dqc_reference
[2023-06-05 02:37:19,309] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:37:19,310] [INFO] Task started: Prodigal
[2023-06-05 02:37:19,311] [INFO] Running command: gunzip -c /var/lib/cwl/stgc125d580-25a9-425d-a711-313125ddbb34/GCA_934547095.1_ERR7746411_bin.236_genomic.fna.gz | prodigal -d GCA_934547095.1_ERR7746411_bin.236_genomic.fna/cds.fna -a GCA_934547095.1_ERR7746411_bin.236_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:37:26,665] [INFO] Task succeeded: Prodigal
[2023-06-05 02:37:26,665] [INFO] Task started: HMMsearch
[2023-06-05 02:37:26,665] [INFO] Running command: hmmsearch --tblout GCA_934547095.1_ERR7746411_bin.236_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e10c052-c889-4f1d-8c7f-3ac8a1854df3/dqc_reference/reference_markers.hmm GCA_934547095.1_ERR7746411_bin.236_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:37:26,899] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:37:26,900] [INFO] Found 6/6 markers.
[2023-06-05 02:37:26,926] [INFO] Query marker FASTA was written to GCA_934547095.1_ERR7746411_bin.236_genomic.fna/markers.fasta
[2023-06-05 02:37:26,927] [INFO] Task started: Blastn
[2023-06-05 02:37:26,927] [INFO] Running command: blastn -query GCA_934547095.1_ERR7746411_bin.236_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e10c052-c889-4f1d-8c7f-3ac8a1854df3/dqc_reference/reference_markers.fasta -out GCA_934547095.1_ERR7746411_bin.236_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:37:27,592] [INFO] Task succeeded: Blastn
[2023-06-05 02:37:27,597] [INFO] Selected 15 target genomes.
[2023-06-05 02:37:27,597] [INFO] Target genome list was writen to GCA_934547095.1_ERR7746411_bin.236_genomic.fna/target_genomes.txt
[2023-06-05 02:37:27,600] [INFO] Task started: fastANI
[2023-06-05 02:37:27,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgc125d580-25a9-425d-a711-313125ddbb34/GCA_934547095.1_ERR7746411_bin.236_genomic.fna.gz --refList GCA_934547095.1_ERR7746411_bin.236_genomic.fna/target_genomes.txt --output GCA_934547095.1_ERR7746411_bin.236_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:37:34,317] [INFO] Task succeeded: fastANI
[2023-06-05 02:37:34,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e10c052-c889-4f1d-8c7f-3ac8a1854df3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:37:34,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e10c052-c889-4f1d-8c7f-3ac8a1854df3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:37:34,330] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:37:34,331] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:37:34,331] [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=JCM 31915	GCA_010509575.1	411483	411483	type	True	78.554	169	748	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	78.5435	169	748	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	78.3661	190	748	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	78.0552	128	748	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	77.678	159	748	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	77.6679	140	748	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	77.3935	178	748	95	below_threshold
Pygmaiobacter massiliensis	strain=Marseille-P3336	GCA_900199435.1	1917873	1917873	type	True	75.9568	53	748	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:37:34,333] [INFO] DFAST Taxonomy check result was written to GCA_934547095.1_ERR7746411_bin.236_genomic.fna/tc_result.tsv
[2023-06-05 02:37:34,333] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:37:34,334] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:37:34,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e10c052-c889-4f1d-8c7f-3ac8a1854df3/dqc_reference/checkm_data
[2023-06-05 02:37:34,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:37:34,360] [INFO] Task started: CheckM
[2023-06-05 02:37:34,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934547095.1_ERR7746411_bin.236_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934547095.1_ERR7746411_bin.236_genomic.fna/checkm_input GCA_934547095.1_ERR7746411_bin.236_genomic.fna/checkm_result
[2023-06-05 02:38:01,147] [INFO] Task succeeded: CheckM
[2023-06-05 02:38:01,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:38:01,168] [INFO] ===== Completeness check finished =====
[2023-06-05 02:38:01,168] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:38:01,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934547095.1_ERR7746411_bin.236_genomic.fna/markers.fasta)
[2023-06-05 02:38:01,169] [INFO] Task started: Blastn
[2023-06-05 02:38:01,169] [INFO] Running command: blastn -query GCA_934547095.1_ERR7746411_bin.236_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e10c052-c889-4f1d-8c7f-3ac8a1854df3/dqc_reference/reference_markers_gtdb.fasta -out GCA_934547095.1_ERR7746411_bin.236_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:38:02,293] [INFO] Task succeeded: Blastn
[2023-06-05 02:38:02,297] [INFO] Selected 24 target genomes.
[2023-06-05 02:38:02,297] [INFO] Target genome list was writen to GCA_934547095.1_ERR7746411_bin.236_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:38:02,305] [INFO] Task started: fastANI
[2023-06-05 02:38:02,305] [INFO] Running command: fastANI --query /var/lib/cwl/stgc125d580-25a9-425d-a711-313125ddbb34/GCA_934547095.1_ERR7746411_bin.236_genomic.fna.gz --refList GCA_934547095.1_ERR7746411_bin.236_genomic.fna/target_genomes_gtdb.txt --output GCA_934547095.1_ERR7746411_bin.236_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:38:13,181] [INFO] Task succeeded: fastANI
[2023-06-05 02:38:13,212] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:38:13,212] [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_004555405.1	s__Gemmiger sp004555405	97.1032	574	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.36	97.23	0.85	0.84	4	conclusive
GCA_900765705.1	s__Faecalibacterium sp900765705	78.6511	143	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.09	97.09	0.66	0.66	2	-
GCF_003287405.1	s__Faecalibacterium prausnitzii_J	78.5063	187	748	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_002549775.1	s__Faecalibacterium prausnitzii_F	78.4816	187	748	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_004555865.1	s__SFJ001 sp004555865	78.3991	222	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__SFJ001	95.0	98.44	98.34	0.90	0.89	3	-
GCF_003324185.1	s__Faecalibacterium prausnitzii	78.3868	189	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.64	96.12	0.86	0.79	47	-
GCF_002550015.1	s__Faecalibacterium prausnitzii_A	78.3321	178	748	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_003287495.1	s__Faecalibacterium prausnitzii_I	78.2976	146	748	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_003449675.1	s__Faecalibacterium sp003449675	78.1189	121	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	96.56	96.55	0.80	0.74	3	-
GCF_002161595.1	s__Fournierella sp002161595	77.9596	159	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	98.81	98.81	0.92	0.92	2	-
GCF_002160955.1	s__Gemmiger_A avium	77.8604	153	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger_A	95.0	98.36	98.15	0.86	0.80	3	-
GCA_004552305.1	s__Gemmiger variabilis_A	77.8516	175	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.82	96.59	0.82	0.70	4	-
GCA_017483235.1	s__Faecalibacterium sp017483235	77.7733	162	748	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_004558805.1	s__Faecalibacterium prausnitzii_M	77.6958	142	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.98	97.83	0.94	0.93	3	-
GCA_017472375.1	s__SFJ001 sp017472375	77.5567	104	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__SFJ001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765105.1	s__Faecalibacterium sp900765105	77.5532	124	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.27	98.27	0.82	0.82	2	-
GCA_905215595.1	s__Faecalibacterium sp905215595	77.4601	118	748	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_900543285.1	s__Fournierella sp900543285	77.4552	146	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	99.38	98.75	0.91	0.84	3	-
GCF_004345265.1	s__Fournierella massiliensis	77.3935	178	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	99.99	99.99	1.00	1.00	3	-
GCA_003343905.1	s__Gemmiger variabilis_C	77.3737	127	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116705.1	s__Gemmiger avistercoris	77.3231	120	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	99.94	99.94	0.92	0.92	2	-
GCA_019115045.1	s__Gemmiger excrementipullorum	77.0835	136	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119365.1	s__Gemmiger stercoripullorum	77.0176	115	748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.12	98.12	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-05 02:38:13,214] [INFO] GTDB search result was written to GCA_934547095.1_ERR7746411_bin.236_genomic.fna/result_gtdb.tsv
[2023-06-05 02:38:13,215] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:38:13,219] [INFO] DFAST_QC result json was written to GCA_934547095.1_ERR7746411_bin.236_genomic.fna/dqc_result.json
[2023-06-05 02:38:13,219] [INFO] DFAST_QC completed!
[2023-06-05 02:38:13,219] [INFO] Total running time: 0h0m55s