[2024-01-24 14:39:45,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:45,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:45,827] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7d1ddd1-f044-47bd-b951-f7433cc10d6e/dqc_reference
[2024-01-24 14:39:48,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:48,366] [INFO] Task started: Prodigal
[2024-01-24 14:39:48,366] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a8c1f78-e140-401f-8f14-4b428aaacc47/GCF_014287705.1_ASM1428770v1_genomic.fna.gz | prodigal -d GCF_014287705.1_ASM1428770v1_genomic.fna/cds.fna -a GCF_014287705.1_ASM1428770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:55,667] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:55,667] [INFO] Task started: HMMsearch
[2024-01-24 14:39:55,668] [INFO] Running command: hmmsearch --tblout GCF_014287705.1_ASM1428770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7d1ddd1-f044-47bd-b951-f7433cc10d6e/dqc_reference/reference_markers.hmm GCF_014287705.1_ASM1428770v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:55,957] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:55,959] [INFO] Found 6/6 markers.
[2024-01-24 14:39:55,991] [INFO] Query marker FASTA was written to GCF_014287705.1_ASM1428770v1_genomic.fna/markers.fasta
[2024-01-24 14:39:55,991] [INFO] Task started: Blastn
[2024-01-24 14:39:55,991] [INFO] Running command: blastn -query GCF_014287705.1_ASM1428770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7d1ddd1-f044-47bd-b951-f7433cc10d6e/dqc_reference/reference_markers.fasta -out GCF_014287705.1_ASM1428770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:56,663] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:56,667] [INFO] Selected 22 target genomes.
[2024-01-24 14:39:56,667] [INFO] Target genome list was writen to GCF_014287705.1_ASM1428770v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:56,686] [INFO] Task started: fastANI
[2024-01-24 14:39:56,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a8c1f78-e140-401f-8f14-4b428aaacc47/GCF_014287705.1_ASM1428770v1_genomic.fna.gz --refList GCF_014287705.1_ASM1428770v1_genomic.fna/target_genomes.txt --output GCF_014287705.1_ASM1428770v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:07,202] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:07,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7d1ddd1-f044-47bd-b951-f7433cc10d6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:07,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7d1ddd1-f044-47bd-b951-f7433cc10d6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:07,231] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:40:07,231] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:40:07,231] [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	81.5854	248	990	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	81.4225	287	990	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	81.1652	288	990	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	80.8684	194	990	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	80.8217	332	990	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	80.7681	334	990	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	80.3457	224	990	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	79.4958	154	990	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	79.4534	179	990	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	79.1115	191	990	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	79.1064	170	990	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	79.051	174	990	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.0471	191	990	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.9436	170	990	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	78.4427	169	990	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	78.4244	139	990	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	78.3681	170	990	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	78.3555	141	990	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	78.2265	181	990	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	76.9645	78	990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:07,233] [INFO] DFAST Taxonomy check result was written to GCF_014287705.1_ASM1428770v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:07,234] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:07,234] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:07,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7d1ddd1-f044-47bd-b951-f7433cc10d6e/dqc_reference/checkm_data
[2024-01-24 14:40:07,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:07,272] [INFO] Task started: CheckM
[2024-01-24 14:40:07,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287705.1_ASM1428770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287705.1_ASM1428770v1_genomic.fna/checkm_input GCF_014287705.1_ASM1428770v1_genomic.fna/checkm_result
[2024-01-24 14:40:35,789] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:35,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:35,818] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:35,819] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:35,820] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287705.1_ASM1428770v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:35,821] [INFO] Task started: Blastn
[2024-01-24 14:40:35,821] [INFO] Running command: blastn -query GCF_014287705.1_ASM1428770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7d1ddd1-f044-47bd-b951-f7433cc10d6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287705.1_ASM1428770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:36,921] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:36,925] [INFO] Selected 16 target genomes.
[2024-01-24 14:40:36,925] [INFO] Target genome list was writen to GCF_014287705.1_ASM1428770v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:36,941] [INFO] Task started: fastANI
[2024-01-24 14:40:36,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a8c1f78-e140-401f-8f14-4b428aaacc47/GCF_014287705.1_ASM1428770v1_genomic.fna.gz --refList GCF_014287705.1_ASM1428770v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287705.1_ASM1428770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:46,152] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:46,174] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:46,174] [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_003435815.1	s__CAG-317 sp000433215	98.4214	824	990	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	conclusive
GCA_902362865.1	s__Lachnoclostridium_B sp900066765	82.1347	207	990	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	-
GCF_001404875.1	s__Dorea_A longicatena_B	81.9051	362	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	-
GCF_000169235.1	s__Dorea formicigenerans	81.4546	286	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea	95.0	97.68	96.97	0.80	0.73	43	-
GCA_000155875.1	s__Bariatricus comes	81.372	238	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCA_003480425.1	s__Schaedlerella sp900066545	81.0663	191	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.16	96.52	0.81	0.77	11	-
GCF_000154065.1	s__Dorea_A longicatena	80.7747	333	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	98.55	97.61	0.85	0.69	49	-
GCF_003477705.1	s__Lachnoclostridium_B sp900066555	80.2334	237	990	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_900550865.1	s__Dorea_A sp900550865	79.2782	260	990	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_000433535.1	s__CAG-317 sp000433535	78.9708	246	990	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	-
GCA_900543415.1	s__CAG-317 sp900543415	78.8936	235	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	97.35	95.87	0.87	0.78	4	-
GCA_910578495.1	s__CAG-317 sp910578495	78.7412	207	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905203555.1	s__Schaedlerella sp905203555	78.6873	127	990	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_001754075.1	s__Merdimonas faecis	78.2479	180	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	98.52	97.96	0.90	0.84	10	-
GCA_900553355.1	s__Merdimonas sp900553355	78.1655	159	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120075.1	s__Mediterraneibacter excrementigallinarum_A	77.0518	90	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.40	96.45	0.78	0.77	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:46,176] [INFO] GTDB search result was written to GCF_014287705.1_ASM1428770v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:46,177] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:46,182] [INFO] DFAST_QC result json was written to GCF_014287705.1_ASM1428770v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:46,182] [INFO] DFAST_QC completed!
[2024-01-24 14:40:46,182] [INFO] Total running time: 0h1m0s