[2023-06-29 16:09:15,121] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:09:15,126] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:09:15,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg1699907c-d49d-438a-b747-60529ce158be/dqc_reference
[2023-06-29 16:09:17,176] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:09:17,178] [INFO] Task started: Prodigal
[2023-06-29 16:09:17,178] [INFO] Running command: gunzip -c /var/lib/cwl/stg2eee4417-8109-445c-b8c5-4fd214560567/GCA_021202845.1_ASM2120284v1_genomic.fna.gz | prodigal -d GCA_021202845.1_ASM2120284v1_genomic.fna/cds.fna -a GCA_021202845.1_ASM2120284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:09:23,262] [INFO] Task succeeded: Prodigal
[2023-06-29 16:09:23,263] [INFO] Task started: HMMsearch
[2023-06-29 16:09:23,263] [INFO] Running command: hmmsearch --tblout GCA_021202845.1_ASM2120284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1699907c-d49d-438a-b747-60529ce158be/dqc_reference/reference_markers.hmm GCA_021202845.1_ASM2120284v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:09:23,514] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:09:23,515] [INFO] Found 6/6 markers.
[2023-06-29 16:09:23,547] [INFO] Query marker FASTA was written to GCA_021202845.1_ASM2120284v1_genomic.fna/markers.fasta
[2023-06-29 16:09:23,548] [INFO] Task started: Blastn
[2023-06-29 16:09:23,548] [INFO] Running command: blastn -query GCA_021202845.1_ASM2120284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1699907c-d49d-438a-b747-60529ce158be/dqc_reference/reference_markers.fasta -out GCA_021202845.1_ASM2120284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:09:24,252] [INFO] Task succeeded: Blastn
[2023-06-29 16:09:24,256] [INFO] Selected 27 target genomes.
[2023-06-29 16:09:24,256] [INFO] Target genome list was writen to GCA_021202845.1_ASM2120284v1_genomic.fna/target_genomes.txt
[2023-06-29 16:09:24,260] [INFO] Task started: fastANI
[2023-06-29 16:09:24,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eee4417-8109-445c-b8c5-4fd214560567/GCA_021202845.1_ASM2120284v1_genomic.fna.gz --refList GCA_021202845.1_ASM2120284v1_genomic.fna/target_genomes.txt --output GCA_021202845.1_ASM2120284v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:09:40,945] [INFO] Task succeeded: fastANI
[2023-06-29 16:09:40,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1699907c-d49d-438a-b747-60529ce158be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:09:40,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1699907c-d49d-438a-b747-60529ce158be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:09:40,960] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:09:40,960] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:09:40,960] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.522	59	730	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.4549	64	730	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.4408	61	730	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.4006	66	730	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.3845	62	730	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.283	66	730	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.0924	51	730	95	below_threshold
Sporobacter termitidis	strain=DSM 10068	GCA_900130065.1	44749	44749	type	True	75.5217	67	730	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:09:40,962] [INFO] DFAST Taxonomy check result was written to GCA_021202845.1_ASM2120284v1_genomic.fna/tc_result.tsv
[2023-06-29 16:09:40,963] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:09:40,963] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:09:40,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1699907c-d49d-438a-b747-60529ce158be/dqc_reference/checkm_data
[2023-06-29 16:09:40,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:09:40,997] [INFO] Task started: CheckM
[2023-06-29 16:09:40,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021202845.1_ASM2120284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021202845.1_ASM2120284v1_genomic.fna/checkm_input GCA_021202845.1_ASM2120284v1_genomic.fna/checkm_result
[2023-06-29 16:10:04,805] [INFO] Task succeeded: CheckM
[2023-06-29 16:10:04,807] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:10:04,829] [INFO] ===== Completeness check finished =====
[2023-06-29 16:10:04,829] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:10:04,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021202845.1_ASM2120284v1_genomic.fna/markers.fasta)
[2023-06-29 16:10:04,830] [INFO] Task started: Blastn
[2023-06-29 16:10:04,830] [INFO] Running command: blastn -query GCA_021202845.1_ASM2120284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1699907c-d49d-438a-b747-60529ce158be/dqc_reference/reference_markers_gtdb.fasta -out GCA_021202845.1_ASM2120284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:10:06,014] [INFO] Task succeeded: Blastn
[2023-06-29 16:10:06,019] [INFO] Selected 31 target genomes.
[2023-06-29 16:10:06,019] [INFO] Target genome list was writen to GCA_021202845.1_ASM2120284v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:10:06,045] [INFO] Task started: fastANI
[2023-06-29 16:10:06,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eee4417-8109-445c-b8c5-4fd214560567/GCA_021202845.1_ASM2120284v1_genomic.fna.gz --refList GCA_021202845.1_ASM2120284v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021202845.1_ASM2120284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:10:17,232] [INFO] Task succeeded: fastANI
[2023-06-29 16:10:17,254] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:10:17,255] [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_900317855.1	s__CAG-103 sp900317855	77.3285	110	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	97.11	95.56	0.88	0.84	11	-
GCA_000432375.1	s__CAG-103 sp000432375	77.1755	98	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.15	97.87	0.87	0.82	10	-
GCA_900543625.1	s__CAG-103 sp900543625	77.1503	104	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.93	95.23	0.89	0.87	12	-
GCA_018265835.1	s__CAG-103 sp018265835	77.1448	105	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757655.1	s__CAG-103 sp900757655	77.0571	100	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.74	95.66	0.88	0.82	7	-
GCA_017430985.1	s__Limivicinus sp017430985	77.0564	88	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068365.1	s__RGIG7114 sp015068365	76.9735	118	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__RGIG7114	95.0	98.05	98.05	0.85	0.85	2	-
GCA_900319465.1	s__Limivicinus sp900319465	76.9665	93	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.77	99.67	0.93	0.92	4	-
GCA_902778115.1	s__Limivicinus sp902778115	76.9581	92	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.60	97.29	0.87	0.83	3	-
GCA_015067435.1	s__ER4 sp015067435	76.9557	97	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543085.1	s__Scatomorpha pullicola	76.9455	138	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	97.83	97.68	0.88	0.83	7	-
GCA_902785905.1	s__Limivicinus sp902785905	76.9453	79	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549645.1	s__Limivicinus sp900549645	76.9028	81	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.52	99.05	0.92	0.86	3	-
GCA_902760845.1	s__CAG-103 sp902760845	76.8964	96	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545405.1	s__Scatomorpha sp900545405	76.8934	133	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	98.32	98.22	0.88	0.84	4	-
GCA_900759385.1	s__Scatomorpha sp900759385	76.8476	117	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	98.68	98.63	0.90	0.88	3	-
GCA_017445985.1	s__RGIG7114 sp017445985	76.7539	80	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__RGIG7114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902790375.1	s__Limivicinus sp902790375	76.7456	78	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712985.1	s__Scatomorpha intestinavium	76.7195	96	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017535865.1	s__Limivicinus sp017535865	76.6626	55	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716005.1	s__Scatomorpha stercoravium	76.6401	93	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713375.1	s__Scatomorpha stercorigallinarum	76.6158	102	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549865.1	s__Limivicinus sp900549865	76.4961	87	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.13	98.09	0.79	0.79	3	-
GCA_902761635.1	s__Limivicinus sp902761635	76.4463	74	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784305.1	s__Onthomonas sp902784305	76.4398	58	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Onthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:10:17,258] [INFO] GTDB search result was written to GCA_021202845.1_ASM2120284v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:10:17,258] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:10:17,263] [INFO] DFAST_QC result json was written to GCA_021202845.1_ASM2120284v1_genomic.fna/dqc_result.json
[2023-06-29 16:10:17,263] [INFO] DFAST_QC completed!
[2023-06-29 16:10:17,263] [INFO] Total running time: 0h1m2s