[2024-01-25 17:39:50,474] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:50,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:50,476] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4025842-8b40-4513-8fa3-8e8e3fc91c18/dqc_reference
[2024-01-25 17:39:51,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:51,577] [INFO] Task started: Prodigal
[2024-01-25 17:39:51,578] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa48581c-8981-49a4-bdd5-f730c4da714c/GCF_003885045.1_ASM388504v1_genomic.fna.gz | prodigal -d GCF_003885045.1_ASM388504v1_genomic.fna/cds.fna -a GCF_003885045.1_ASM388504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:06,671] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:06,672] [INFO] Task started: HMMsearch
[2024-01-25 17:40:06,672] [INFO] Running command: hmmsearch --tblout GCF_003885045.1_ASM388504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4025842-8b40-4513-8fa3-8e8e3fc91c18/dqc_reference/reference_markers.hmm GCF_003885045.1_ASM388504v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:06,970] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:06,971] [INFO] Found 6/6 markers.
[2024-01-25 17:40:07,022] [INFO] Query marker FASTA was written to GCF_003885045.1_ASM388504v1_genomic.fna/markers.fasta
[2024-01-25 17:40:07,022] [INFO] Task started: Blastn
[2024-01-25 17:40:07,022] [INFO] Running command: blastn -query GCF_003885045.1_ASM388504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4025842-8b40-4513-8fa3-8e8e3fc91c18/dqc_reference/reference_markers.fasta -out GCF_003885045.1_ASM388504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:07,651] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:07,654] [INFO] Selected 25 target genomes.
[2024-01-25 17:40:07,655] [INFO] Target genome list was writen to GCF_003885045.1_ASM388504v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:07,686] [INFO] Task started: fastANI
[2024-01-25 17:40:07,686] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa48581c-8981-49a4-bdd5-f730c4da714c/GCF_003885045.1_ASM388504v1_genomic.fna.gz --refList GCF_003885045.1_ASM388504v1_genomic.fna/target_genomes.txt --output GCF_003885045.1_ASM388504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:24,922] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:24,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4025842-8b40-4513-8fa3-8e8e3fc91c18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:24,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4025842-8b40-4513-8fa3-8e8e3fc91c18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:24,937] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:24,943] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:24,943] [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
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	100.0	2172	2172	95	conclusive
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	80.7559	142	2172	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.8783	94	2172	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	78.3682	88	2172	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.1835	111	2172	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.1168	113	2172	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	78.0812	167	2172	95	below_threshold
Luxibacter massiliensis	strain=Marseille-P5551	GCA_900604355.1	2219695	2219695	type	True	77.9878	144	2172	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	77.9683	92	2172	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.8602	166	2172	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	77.8017	143	2172	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	77.7861	70	2172	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	77.6842	134	2172	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.6015	171	2172	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.5776	168	2172	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	77.5097	147	2172	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.48	174	2172	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.329	166	2172	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	77.3098	68	2172	95	below_threshold
Muricomes intestini	strain=DSM 29489	GCA_004346165.1	1796634	1796634	type	True	77.0944	105	2172	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	77.0593	95	2172	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	76.9277	109	2172	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.5788	86	2172	95	below_threshold
Hespellia stercorisuis	strain=DSM 15480	GCA_900142165.1	180311	180311	type	True	76.4564	117	2172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:24,947] [INFO] DFAST Taxonomy check result was written to GCF_003885045.1_ASM388504v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:24,948] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:24,948] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:24,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4025842-8b40-4513-8fa3-8e8e3fc91c18/dqc_reference/checkm_data
[2024-01-25 17:40:24,949] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:25,020] [INFO] Task started: CheckM
[2024-01-25 17:40:25,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003885045.1_ASM388504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003885045.1_ASM388504v1_genomic.fna/checkm_input GCF_003885045.1_ASM388504v1_genomic.fna/checkm_result
[2024-01-25 17:41:10,376] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:10,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:10,402] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:10,402] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:10,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003885045.1_ASM388504v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:10,403] [INFO] Task started: Blastn
[2024-01-25 17:41:10,403] [INFO] Running command: blastn -query GCF_003885045.1_ASM388504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4025842-8b40-4513-8fa3-8e8e3fc91c18/dqc_reference/reference_markers_gtdb.fasta -out GCF_003885045.1_ASM388504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:11,530] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:11,541] [INFO] Selected 7 target genomes.
[2024-01-25 17:41:11,541] [INFO] Target genome list was writen to GCF_003885045.1_ASM388504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:11,550] [INFO] Task started: fastANI
[2024-01-25 17:41:11,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa48581c-8981-49a4-bdd5-f730c4da714c/GCF_003885045.1_ASM388504v1_genomic.fna.gz --refList GCF_003885045.1_ASM388504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003885045.1_ASM388504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:21,559] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:21,565] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:21,565] [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_003885045.1	s__Schaedlerella arabinosiphila	100.0	2172	2172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.52	96.80	0.74	0.68	10	conclusive
GCA_009911175.1	s__Schaedlerella sp009911175	87.0758	1207	2172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.09	98.08	0.79	0.79	3	-
GCA_000403295.2	s__Schaedlerella sp000403295	86.8412	1147	2172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.10	98.10	0.85	0.85	2	-
GCA_910575475.1	s__Schaedlerella sp910575475	85.4025	1143	2172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.35	99.35	0.93	0.93	2	-
GCA_009774255.1	s__Schaedlerella sp009774255	81.624	851	2172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900751785.1	s__Mediterraneibacter faecigallinarum	77.3077	164	2172	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_910585995.1	s__Choladocola sp910585995	76.6208	73	2172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:21,566] [INFO] GTDB search result was written to GCF_003885045.1_ASM388504v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:21,567] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:21,572] [INFO] DFAST_QC result json was written to GCF_003885045.1_ASM388504v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:21,572] [INFO] DFAST_QC completed!
[2024-01-25 17:41:21,572] [INFO] Total running time: 0h1m31s