[2024-01-24 12:44:08,537] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:08,539] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:08,539] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0cd7b36-621a-48d8-abf1-bc447bad46e3/dqc_reference
[2024-01-24 12:44:09,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:09,868] [INFO] Task started: Prodigal
[2024-01-24 12:44:09,869] [INFO] Running command: gunzip -c /var/lib/cwl/stgcad6966f-8e2f-4b35-9615-7368d8fd37c8/GCF_003574295.1_ASM357429v1_genomic.fna.gz | prodigal -d GCF_003574295.1_ASM357429v1_genomic.fna/cds.fna -a GCF_003574295.1_ASM357429v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:17,783] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:17,783] [INFO] Task started: HMMsearch
[2024-01-24 12:44:17,783] [INFO] Running command: hmmsearch --tblout GCF_003574295.1_ASM357429v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0cd7b36-621a-48d8-abf1-bc447bad46e3/dqc_reference/reference_markers.hmm GCF_003574295.1_ASM357429v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:18,111] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:18,114] [INFO] Found 6/6 markers.
[2024-01-24 12:44:18,145] [INFO] Query marker FASTA was written to GCF_003574295.1_ASM357429v1_genomic.fna/markers.fasta
[2024-01-24 12:44:18,145] [INFO] Task started: Blastn
[2024-01-24 12:44:18,146] [INFO] Running command: blastn -query GCF_003574295.1_ASM357429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0cd7b36-621a-48d8-abf1-bc447bad46e3/dqc_reference/reference_markers.fasta -out GCF_003574295.1_ASM357429v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:18,810] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:18,814] [INFO] Selected 17 target genomes.
[2024-01-24 12:44:18,814] [INFO] Target genome list was writen to GCF_003574295.1_ASM357429v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:18,877] [INFO] Task started: fastANI
[2024-01-24 12:44:18,878] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad6966f-8e2f-4b35-9615-7368d8fd37c8/GCF_003574295.1_ASM357429v1_genomic.fna.gz --refList GCF_003574295.1_ASM357429v1_genomic.fna/target_genomes.txt --output GCF_003574295.1_ASM357429v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:28,562] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:28,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0cd7b36-621a-48d8-abf1-bc447bad46e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:28,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0cd7b36-621a-48d8-abf1-bc447bad46e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:28,577] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:28,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:28,577] [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
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	100.0	1006	1007	95	conclusive
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	82.3592	200	1007	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	81.0879	221	1007	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	80.844	219	1007	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	80.4726	127	1007	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	80.4092	220	1007	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	80.298	215	1007	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	80.1394	206	1007	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	80.0978	223	1007	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	80.0898	201	1007	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	79.8062	99	1007	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	79.6791	215	1007	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	79.449	106	1007	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	79.1992	136	1007	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	78.5226	119	1007	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.9687	111	1007	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:28,579] [INFO] DFAST Taxonomy check result was written to GCF_003574295.1_ASM357429v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:28,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:28,580] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:28,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0cd7b36-621a-48d8-abf1-bc447bad46e3/dqc_reference/checkm_data
[2024-01-24 12:44:28,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:28,616] [INFO] Task started: CheckM
[2024-01-24 12:44:28,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003574295.1_ASM357429v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003574295.1_ASM357429v1_genomic.fna/checkm_input GCF_003574295.1_ASM357429v1_genomic.fna/checkm_result
[2024-01-24 12:44:58,558] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:58,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:58,578] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:58,578] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:58,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003574295.1_ASM357429v1_genomic.fna/markers.fasta)
[2024-01-24 12:44:58,579] [INFO] Task started: Blastn
[2024-01-24 12:44:58,579] [INFO] Running command: blastn -query GCF_003574295.1_ASM357429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0cd7b36-621a-48d8-abf1-bc447bad46e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003574295.1_ASM357429v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:59,699] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:59,702] [INFO] Selected 22 target genomes.
[2024-01-24 12:44:59,703] [INFO] Target genome list was writen to GCF_003574295.1_ASM357429v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:59,739] [INFO] Task started: fastANI
[2024-01-24 12:44:59,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad6966f-8e2f-4b35-9615-7368d8fd37c8/GCF_003574295.1_ASM357429v1_genomic.fna.gz --refList GCF_003574295.1_ASM357429v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003574295.1_ASM357429v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:10,772] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:10,793] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:10,793] [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_003574295.1	s__Mediterraneibacter_A butyricigenes	100.0	1007	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter_A	95.0	98.15	98.07	0.82	0.80	5	conclusive
GCA_003480425.1	s__Schaedlerella sp900066545	81.6726	179	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.16	96.52	0.81	0.77	11	-
GCA_001312505.1	s__Mediterraneibacter faecis	80.957	197	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.72	95.03	0.76	0.67	61	-
GCF_003435815.1	s__CAG-317 sp000433215	80.5714	189	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCA_000155875.1	s__Bariatricus comes	80.2705	189	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCF_008121495.1	s__Ruminococcus_B gnavus	80.1125	222	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	98.58	96.13	0.80	0.66	102	-
GCF_000155205.1	s__Mediterraneibacter lactaris	80.0775	201	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCF_003477705.1	s__Lachnoclostridium_B sp900066555	79.8714	175	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	97.98	96.92	0.87	0.81	6	-
GCA_002320245.1	s__Schaedlerella sp002320245	78.8375	139	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240315.1	s__Dorea_B phocaeensis	78.4592	117	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_B	95.0	98.22	97.28	0.87	0.81	8	-
GCF_015560805.1	s__Schaedlerella glycyrrhizinilytica_A	78.3041	175	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.33	97.63	0.90	0.83	10	-
GCA_900544395.1	s__Ruminococcus_B sp900544395	78.1345	155	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	99.21	99.21	0.88	0.88	2	-
GCA_900765975.1	s__Schaedlerella sp900765975	78.1331	120	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.94	99.94	0.80	0.80	2	-
GCA_905203555.1	s__Schaedlerella sp905203555	78.046	127	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550865.1	s__Dorea_A sp900550865	77.651	147	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115765.1	s__Mediterraneibacter stercoripullorum	77.458	114	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.91	99.91	0.91	0.91	2	-
GCA_900541505.1	s__Mediterraneibacter sp900541505	77.4322	102	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.61	98.61	0.89	0.89	2	-
GCA_019119995.1	s__Mediterraneibacter faecavium	77.3721	104	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.90	99.90	0.92	0.92	2	-
GCA_900315735.1	s__RUG115 sp900315735	77.2118	88	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	99.35	98.93	0.92	0.85	5	-
GCA_019119745.1	s__Mediterraneibacter gallistercoris	77.0388	86	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118885.1	s__Mediterraneibacter surreyensis	76.7708	103	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.86	98.12	0.80	0.76	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:10,799] [INFO] GTDB search result was written to GCF_003574295.1_ASM357429v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:10,800] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:10,807] [INFO] DFAST_QC result json was written to GCF_003574295.1_ASM357429v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:10,808] [INFO] DFAST_QC completed!
[2024-01-24 12:45:10,808] [INFO] Total running time: 0h1m2s