[2024-01-24 13:33:41,097] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:41,098] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:41,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg86c10a1f-46c7-423a-b6d2-0aa2b490b87a/dqc_reference
[2024-01-24 13:33:42,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:42,379] [INFO] Task started: Prodigal
[2024-01-24 13:33:42,380] [INFO] Running command: gunzip -c /var/lib/cwl/stg00997ac9-979f-4967-ae3d-681df339e283/GCF_030296775.1_ASM3029677v1_genomic.fna.gz | prodigal -d GCF_030296775.1_ASM3029677v1_genomic.fna/cds.fna -a GCF_030296775.1_ASM3029677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:50,146] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:50,147] [INFO] Task started: HMMsearch
[2024-01-24 13:33:50,147] [INFO] Running command: hmmsearch --tblout GCF_030296775.1_ASM3029677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86c10a1f-46c7-423a-b6d2-0aa2b490b87a/dqc_reference/reference_markers.hmm GCF_030296775.1_ASM3029677v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:50,422] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:50,423] [INFO] Found 6/6 markers.
[2024-01-24 13:33:50,455] [INFO] Query marker FASTA was written to GCF_030296775.1_ASM3029677v1_genomic.fna/markers.fasta
[2024-01-24 13:33:50,456] [INFO] Task started: Blastn
[2024-01-24 13:33:50,456] [INFO] Running command: blastn -query GCF_030296775.1_ASM3029677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86c10a1f-46c7-423a-b6d2-0aa2b490b87a/dqc_reference/reference_markers.fasta -out GCF_030296775.1_ASM3029677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:51,140] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:51,143] [INFO] Selected 26 target genomes.
[2024-01-24 13:33:51,143] [INFO] Target genome list was writen to GCF_030296775.1_ASM3029677v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:51,292] [INFO] Task started: fastANI
[2024-01-24 13:33:51,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg00997ac9-979f-4967-ae3d-681df339e283/GCF_030296775.1_ASM3029677v1_genomic.fna.gz --refList GCF_030296775.1_ASM3029677v1_genomic.fna/target_genomes.txt --output GCF_030296775.1_ASM3029677v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:34:06,253] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:06,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86c10a1f-46c7-423a-b6d2-0aa2b490b87a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:34:06,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86c10a1f-46c7-423a-b6d2-0aa2b490b87a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:34:06,276] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:34:06,276] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:34:06,276] [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 catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	79.2897	112	1037	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	79.0275	109	1037	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	79.0072	92	1037	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	78.8209	175	1037	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	78.7656	142	1037	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	78.6659	142	1037	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	78.6216	171	1037	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	78.5892	81	1037	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	78.5681	132	1037	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.5606	142	1037	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	78.5602	95	1037	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_008281175.1	89153	89153	type	True	78.5177	140	1037	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	78.4325	152	1037	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	78.4035	144	1037	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	78.3885	139	1037	95	below_threshold
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	78.3868	128	1037	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	78.3847	107	1037	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	78.219	143	1037	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	78.1392	150	1037	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.1283	115	1037	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	78.0461	103	1037	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	78.0372	145	1037	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	78.0105	136	1037	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.833	132	1037	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.378	104	1037	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	77.0312	62	1037	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:34:06,278] [INFO] DFAST Taxonomy check result was written to GCF_030296775.1_ASM3029677v1_genomic.fna/tc_result.tsv
[2024-01-24 13:34:06,279] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:34:06,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:34:06,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86c10a1f-46c7-423a-b6d2-0aa2b490b87a/dqc_reference/checkm_data
[2024-01-24 13:34:06,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:34:06,311] [INFO] Task started: CheckM
[2024-01-24 13:34:06,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030296775.1_ASM3029677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030296775.1_ASM3029677v1_genomic.fna/checkm_input GCF_030296775.1_ASM3029677v1_genomic.fna/checkm_result
[2024-01-24 13:34:34,917] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:34,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:34,940] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:34,941] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:34,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030296775.1_ASM3029677v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:34,942] [INFO] Task started: Blastn
[2024-01-24 13:34:34,942] [INFO] Running command: blastn -query GCF_030296775.1_ASM3029677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86c10a1f-46c7-423a-b6d2-0aa2b490b87a/dqc_reference/reference_markers_gtdb.fasta -out GCF_030296775.1_ASM3029677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:36,042] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:36,046] [INFO] Selected 23 target genomes.
[2024-01-24 13:34:36,047] [INFO] Target genome list was writen to GCF_030296775.1_ASM3029677v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:36,190] [INFO] Task started: fastANI
[2024-01-24 13:34:36,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg00997ac9-979f-4967-ae3d-681df339e283/GCF_030296775.1_ASM3029677v1_genomic.fna.gz --refList GCF_030296775.1_ASM3029677v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030296775.1_ASM3029677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:47,111] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:47,130] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:47,131] [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_900543315.1	s__Lachnoclostridium_B faecipullorum	98.2941	772	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	98.64	98.13	0.82	0.72	5	conclusive
GCF_900120345.1	s__Lachnoclostridium_B phocaeense	80.6634	324	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	98.08	98.08	0.84	0.84	2	-
GCF_002160985.1	s__Lachnoclostridium_B stercoravium	80.3043	272	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	98.37	98.26	0.93	0.92	3	-
GCF_000765215.1	s__Lachnoclostridium_B sp000765215	79.5798	279	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	98.26	97.36	0.89	0.84	10	-
GCF_016901695.1	s__Lachnoclostridium_B massiliensis_A	79.2116	209	1037	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	-
GCF_008121495.1	s__Ruminococcus_B gnavus	78.4772	142	1037	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_008281175.1	s__Extibacter hylemonae	78.4645	140	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	99.20	98.44	0.97	0.93	5	-
GCF_003574295.1	s__Mediterraneibacter_A butyricigenes	78.3996	130	1037	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	-
GCF_900240315.1	s__Dorea_B phocaeensis	78.1639	149	1037	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_019113645.1	s__Mediterraneibacter vanvlietii	78.0465	122	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.04	97.81	0.84	0.83	3	-
GCF_000153925.1	s__Mediterraneibacter torques	78.0117	104	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.42	99.19	0.88	0.82	25	-
GCF_003477705.1	s__Lachnoclostridium_B sp900066555	77.9329	148	1037	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	-
GCF_013300725.1	s__Bariatricus comes_A	77.7781	138	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCA_900550865.1	s__Dorea_A sp900550865	77.4324	123	1037	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_019119205.1	s__Mediterraneibacter intestinavium	77.3755	80	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.10	98.10	0.78	0.78	2	-
GCA_910585725.1	s__Sporofaciens sp910585725	77.3336	113	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002492335.1	s__UBA7109 sp002492335	77.2743	91	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119745.1	s__Mediterraneibacter gallistercoris	77.1224	86	1037	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_900556835.1	s__Faecalimonas sp900556835	75.7699	68	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:47,132] [INFO] GTDB search result was written to GCF_030296775.1_ASM3029677v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:47,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:47,137] [INFO] DFAST_QC result json was written to GCF_030296775.1_ASM3029677v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:47,137] [INFO] DFAST_QC completed!
[2024-01-24 13:34:47,137] [INFO] Total running time: 0h1m6s