[2024-01-24 12:48:04,875] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:48:04,877] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:48:04,877] [INFO] DQC Reference Directory: /var/lib/cwl/stg40780aa6-2da5-484c-8457-61dca2060c1b/dqc_reference
[2024-01-24 12:48:06,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:48:06,098] [INFO] Task started: Prodigal
[2024-01-24 12:48:06,099] [INFO] Running command: gunzip -c /var/lib/cwl/stgad328844-3f74-4fc7-b67b-722834d48b14/GCF_020687545.1_ASM2068754v1_genomic.fna.gz | prodigal -d GCF_020687545.1_ASM2068754v1_genomic.fna/cds.fna -a GCF_020687545.1_ASM2068754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:15,540] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:15,541] [INFO] Task started: HMMsearch
[2024-01-24 12:48:15,541] [INFO] Running command: hmmsearch --tblout GCF_020687545.1_ASM2068754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40780aa6-2da5-484c-8457-61dca2060c1b/dqc_reference/reference_markers.hmm GCF_020687545.1_ASM2068754v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:15,885] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:15,886] [INFO] Found 6/6 markers.
[2024-01-24 12:48:15,921] [INFO] Query marker FASTA was written to GCF_020687545.1_ASM2068754v1_genomic.fna/markers.fasta
[2024-01-24 12:48:15,921] [INFO] Task started: Blastn
[2024-01-24 12:48:15,921] [INFO] Running command: blastn -query GCF_020687545.1_ASM2068754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40780aa6-2da5-484c-8457-61dca2060c1b/dqc_reference/reference_markers.fasta -out GCF_020687545.1_ASM2068754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:16,580] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:16,584] [INFO] Selected 22 target genomes.
[2024-01-24 12:48:16,585] [INFO] Target genome list was writen to GCF_020687545.1_ASM2068754v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:16,592] [INFO] Task started: fastANI
[2024-01-24 12:48:16,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgad328844-3f74-4fc7-b67b-722834d48b14/GCF_020687545.1_ASM2068754v1_genomic.fna.gz --refList GCF_020687545.1_ASM2068754v1_genomic.fna/target_genomes.txt --output GCF_020687545.1_ASM2068754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:28,414] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:28,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40780aa6-2da5-484c-8457-61dca2060c1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:28,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40780aa6-2da5-484c-8457-61dca2060c1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:28,431] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:48:28,432] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:48:28,432] [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
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	82.993	175	1220	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	79.7397	349	1220	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.4657	158	1220	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.4601	160	1220	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	78.4398	184	1220	95	below_threshold
Sellimonas caecigallum	strain=SW451	GCA_019754295.1	2592333	2592333	type	True	77.943	112	1220	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.9316	163	1220	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.9302	165	1220	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	77.9212	162	1220	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.9145	167	1220	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.7309	146	1220	95	below_threshold
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	77.5098	85	1220	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	77.4311	94	1220	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.3624	178	1220	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.3342	91	1220	95	below_threshold
Muricomes intestini	strain=DSM 29489	GCA_004346165.1	1796634	1796634	type	True	76.9913	87	1220	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.8746	63	1220	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:28,434] [INFO] DFAST Taxonomy check result was written to GCF_020687545.1_ASM2068754v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:28,435] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:28,435] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:28,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40780aa6-2da5-484c-8457-61dca2060c1b/dqc_reference/checkm_data
[2024-01-24 12:48:28,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:28,482] [INFO] Task started: CheckM
[2024-01-24 12:48:28,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020687545.1_ASM2068754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020687545.1_ASM2068754v1_genomic.fna/checkm_input GCF_020687545.1_ASM2068754v1_genomic.fna/checkm_result
[2024-01-24 12:49:02,071] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:02,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:02,100] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:02,100] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:02,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020687545.1_ASM2068754v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:02,101] [INFO] Task started: Blastn
[2024-01-24 12:49:02,102] [INFO] Running command: blastn -query GCF_020687545.1_ASM2068754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40780aa6-2da5-484c-8457-61dca2060c1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_020687545.1_ASM2068754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:03,170] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:03,175] [INFO] Selected 22 target genomes.
[2024-01-24 12:49:03,175] [INFO] Target genome list was writen to GCF_020687545.1_ASM2068754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:03,215] [INFO] Task started: fastANI
[2024-01-24 12:49:03,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgad328844-3f74-4fc7-b67b-722834d48b14/GCF_020687545.1_ASM2068754v1_genomic.fna.gz --refList GCF_020687545.1_ASM2068754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020687545.1_ASM2068754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:14,309] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:14,332] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:49:14,333] [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_002161355.1	s__Mediterraneibacter caccavium	80.8772	372	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.91	97.67	0.90	0.86	7	-
GCF_002160525.1	s__Mediterraneibacter cottocaccae	80.7263	402	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.81	98.78	0.88	0.86	3	-
GCF_016902345.1	s__Mediterraneibacter glycyrrhizinilyticus_A	80.2926	381	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159505.1	s__Mediterraneibacter ornithocaccae	80.0794	343	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.93	97.52	0.83	0.82	3	-
GCA_019113645.1	s__Mediterraneibacter vanvlietii	79.4863	379	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.04	97.81	0.84	0.83	3	-
GCA_019119995.1	s__Mediterraneibacter faecavium	79.3657	339	1220	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_019112735.1	s__Mediterraneibacter guildfordensis	79.2297	308	1220	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_019120595.1	s__Mediterraneibacter tabaqchaliae	79.1507	277	1220	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_900555215.1	s__Mediterraneibacter excrementipullorum	79.123	181	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.77	95.69	0.82	0.72	8	-
GCA_904377845.1	s__Mediterraneibacter sp904377845	79.0295	315	1220	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_019120575.1	s__Mediterraneibacter quadrami	78.8766	306	1220	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_900751785.1	s__Mediterraneibacter faecigallinarum	78.864	283	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.56	97.84	0.86	0.78	4	-
GCA_019118885.1	s__Mediterraneibacter surreyensis	78.8009	326	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.86	98.12	0.80	0.76	3	-
GCA_019116185.1	s__Mediterraneibacter stercorigallinarum	78.7461	242	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.63	98.63	0.78	0.78	2	-
GCA_019114745.1	s__Mediterraneibacter colneyensis	78.7226	261	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.74	98.74	0.84	0.84	2	-
GCA_019119745.1	s__Mediterraneibacter gallistercoris	78.7066	283	1220	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_019119205.1	s__Mediterraneibacter intestinavium	78.6996	269	1220	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_019120075.1	s__Mediterraneibacter excrementigallinarum_A	78.6917	283	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.40	96.45	0.78	0.77	3	-
GCA_019115385.1	s__Mediterraneibacter avicola	78.6675	243	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.73	98.73	0.86	0.86	2	-
GCA_019118665.1	s__Mediterraneibacter intestinipullorum	78.5774	266	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.27	99.27	0.86	0.86	2	-
GCF_000153925.1	s__Mediterraneibacter torques	78.4269	184	1220	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_001028025.1	s__Muricomes fissicatena_A	77.6387	138	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	99.01	99.01	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:14,334] [INFO] GTDB search result was written to GCF_020687545.1_ASM2068754v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:14,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:14,339] [INFO] DFAST_QC result json was written to GCF_020687545.1_ASM2068754v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:14,339] [INFO] DFAST_QC completed!
[2024-01-24 12:49:14,339] [INFO] Total running time: 0h1m9s