[2024-01-25 17:58:50,608] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:50,610] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:50,610] [INFO] DQC Reference Directory: /var/lib/cwl/stgeedb600b-690b-4fb7-994f-e9c5c34bf2a8/dqc_reference
[2024-01-25 17:58:51,742] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:51,743] [INFO] Task started: Prodigal
[2024-01-25 17:58:51,743] [INFO] Running command: gunzip -c /var/lib/cwl/stgb04512be-f070-415e-b048-61622085ea21/GCF_025567385.1_ASM2556738v1_genomic.fna.gz | prodigal -d GCF_025567385.1_ASM2556738v1_genomic.fna/cds.fna -a GCF_025567385.1_ASM2556738v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:58:59,489] [INFO] Task succeeded: Prodigal
[2024-01-25 17:58:59,489] [INFO] Task started: HMMsearch
[2024-01-25 17:58:59,489] [INFO] Running command: hmmsearch --tblout GCF_025567385.1_ASM2556738v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeedb600b-690b-4fb7-994f-e9c5c34bf2a8/dqc_reference/reference_markers.hmm GCF_025567385.1_ASM2556738v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:58:59,712] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:58:59,713] [INFO] Found 6/6 markers.
[2024-01-25 17:58:59,742] [INFO] Query marker FASTA was written to GCF_025567385.1_ASM2556738v1_genomic.fna/markers.fasta
[2024-01-25 17:58:59,742] [INFO] Task started: Blastn
[2024-01-25 17:58:59,743] [INFO] Running command: blastn -query GCF_025567385.1_ASM2556738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeedb600b-690b-4fb7-994f-e9c5c34bf2a8/dqc_reference/reference_markers.fasta -out GCF_025567385.1_ASM2556738v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:00,322] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:00,324] [INFO] Selected 26 target genomes.
[2024-01-25 17:59:00,325] [INFO] Target genome list was writen to GCF_025567385.1_ASM2556738v1_genomic.fna/target_genomes.txt
[2024-01-25 17:59:00,333] [INFO] Task started: fastANI
[2024-01-25 17:59:00,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgb04512be-f070-415e-b048-61622085ea21/GCF_025567385.1_ASM2556738v1_genomic.fna.gz --refList GCF_025567385.1_ASM2556738v1_genomic.fna/target_genomes.txt --output GCF_025567385.1_ASM2556738v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:14,162] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:14,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeedb600b-690b-4fb7-994f-e9c5c34bf2a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:14,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeedb600b-690b-4fb7-994f-e9c5c34bf2a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:14,175] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:59:14,175] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:59:14,175] [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
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	81.6638	176	1209	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	81.459	159	1209	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	81.0591	115	1209	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	80.6692	89	1209	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	80.5608	180	1209	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	80.4872	182	1209	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	80.1399	130	1209	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	80.1363	129	1209	95	below_threshold
Luxibacter massiliensis	strain=Marseille-P5551	GCA_900604355.1	2219695	2219695	type	True	79.7445	123	1209	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	79.5567	140	1209	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	79.4414	184	1209	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	79.1138	124	1209	95	below_threshold
Sellimonas intestinalis	strain=BR72	GCA_001280875.1	1653434	1653434	type	True	79.047	108	1209	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	78.6187	152	1209	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.6114	128	1209	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	78.5496	150	1209	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	78.5333	170	1209	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.5221	130	1209	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	77.9341	74	1209	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	77.6897	75	1209	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	77.6677	80	1209	95	below_threshold
Sellimonas caecigallum	strain=SW451	GCA_019754295.1	2592333	2592333	type	True	77.5913	83	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:14,176] [INFO] DFAST Taxonomy check result was written to GCF_025567385.1_ASM2556738v1_genomic.fna/tc_result.tsv
[2024-01-25 17:59:14,177] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:14,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:14,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeedb600b-690b-4fb7-994f-e9c5c34bf2a8/dqc_reference/checkm_data
[2024-01-25 17:59:14,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:14,218] [INFO] Task started: CheckM
[2024-01-25 17:59:14,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567385.1_ASM2556738v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567385.1_ASM2556738v1_genomic.fna/checkm_input GCF_025567385.1_ASM2556738v1_genomic.fna/checkm_result
[2024-01-25 17:59:41,091] [INFO] Task succeeded: CheckM
[2024-01-25 17:59:41,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:59:41,109] [INFO] ===== Completeness check finished =====
[2024-01-25 17:59:41,110] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:59:41,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567385.1_ASM2556738v1_genomic.fna/markers.fasta)
[2024-01-25 17:59:41,110] [INFO] Task started: Blastn
[2024-01-25 17:59:41,110] [INFO] Running command: blastn -query GCF_025567385.1_ASM2556738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeedb600b-690b-4fb7-994f-e9c5c34bf2a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567385.1_ASM2556738v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:42,176] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:42,179] [INFO] Selected 24 target genomes.
[2024-01-25 17:59:42,179] [INFO] Target genome list was writen to GCF_025567385.1_ASM2556738v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:59:42,210] [INFO] Task started: fastANI
[2024-01-25 17:59:42,210] [INFO] Running command: fastANI --query /var/lib/cwl/stgb04512be-f070-415e-b048-61622085ea21/GCF_025567385.1_ASM2556738v1_genomic.fna.gz --refList GCF_025567385.1_ASM2556738v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567385.1_ASM2556738v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:59:55,713] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:55,726] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:59:55,727] [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_902362865.1	s__Lachnoclostridium_B sp900066765	100.0	1207	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	99.93	99.86	0.98	0.97	3	conclusive
GCA_001312505.1	s__Mediterraneibacter faecis	82.4405	142	1209	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_900104635.1	s__Faecalimonas phoceensis	81.548	157	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.10	95.01	0.81	0.60	21	-
GCF_000169235.1	s__Dorea formicigenerans	80.52	181	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea	95.0	97.68	96.97	0.80	0.73	43	-
GCF_018228665.1	s__UBA9414 sp003458885	80.1694	148	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	97.84	97.84	0.85	0.85	3	-
GCF_003435815.1	s__CAG-317 sp000433215	79.7942	174	1209	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	-
GCF_900604355.1	s__Luxibacter massiliensis	79.7775	121	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Luxibacter	95.0	99.05	99.03	0.91	0.91	3	-
GCF_900240315.1	s__Dorea_B phocaeensis	79.4297	184	1209	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	-
GCA_910584265.1	s__Lachnoclostridium_B sp910584265	77.7951	174	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584095.1	s__Lachnoclostridium_B sp910584095	77.727	146	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574185.1	s__Lachnoclostridium_B sp910574185	77.7231	177	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433535.1	s__CAG-317 sp000433535	77.6605	160	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.49	98.19	0.84	0.83	3	-
GCF_002159995.1	s__Sellimonas sp002159995	77.5261	93	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sellimonas	95.0	99.10	98.94	0.88	0.83	3	-
GCA_910579015.1	s__Sporofaciens sp910579015	77.5235	113	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028025.1	s__Muricomes fissicatena_A	77.3701	114	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	99.01	99.01	0.90	0.90	3	-
GCA_018365895.1	s__UBA9414 sp018365895	77.3397	92	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588745.1	s__Lachnoclostridium_B sp910588745	77.2621	129	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589275.1	s__Lachnoclostridium_B sp910589275	77.1902	165	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902406105.1	s__Massilistercora sp902406105	77.0684	120	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Massilistercora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905197485.1	s__Faecalimonas sp900555395	77.0042	83	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	100.00	100.00	0.94	0.94	2	-
GCA_905209865.1	s__Mediterraneibacter sp900752395	76.5766	72	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.94	99.94	0.94	0.94	2	-
GCA_900549995.1	s__UMGS1251 sp900549995	76.3846	115	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1251	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904377845.1	s__Mediterraneibacter sp904377845	76.2738	93	1209	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:59:55,728] [INFO] GTDB search result was written to GCF_025567385.1_ASM2556738v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:59:55,728] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:59:55,733] [INFO] DFAST_QC result json was written to GCF_025567385.1_ASM2556738v1_genomic.fna/dqc_result.json
[2024-01-25 17:59:55,733] [INFO] DFAST_QC completed!
[2024-01-25 17:59:55,733] [INFO] Total running time: 0h1m5s