[2023-06-28 17:35:52,651] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:35:52,656] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:35:52,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg10e6e960-11bd-480e-bdfd-02c6cf6607bb/dqc_reference
[2023-06-28 17:35:53,994] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:35:53,996] [INFO] Task started: Prodigal
[2023-06-28 17:35:53,996] [INFO] Running command: gunzip -c /var/lib/cwl/stg8904f517-b2cc-4b5a-8744-61f898ed8790/GCA_019118545.1_ASM1911854v1_genomic.fna.gz | prodigal -d GCA_019118545.1_ASM1911854v1_genomic.fna/cds.fna -a GCA_019118545.1_ASM1911854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:36:00,629] [INFO] Task succeeded: Prodigal
[2023-06-28 17:36:00,629] [INFO] Task started: HMMsearch
[2023-06-28 17:36:00,629] [INFO] Running command: hmmsearch --tblout GCA_019118545.1_ASM1911854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10e6e960-11bd-480e-bdfd-02c6cf6607bb/dqc_reference/reference_markers.hmm GCA_019118545.1_ASM1911854v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:36:00,881] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:36:00,887] [INFO] Found 6/6 markers.
[2023-06-28 17:36:00,918] [INFO] Query marker FASTA was written to GCA_019118545.1_ASM1911854v1_genomic.fna/markers.fasta
[2023-06-28 17:36:00,918] [INFO] Task started: Blastn
[2023-06-28 17:36:00,918] [INFO] Running command: blastn -query GCA_019118545.1_ASM1911854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10e6e960-11bd-480e-bdfd-02c6cf6607bb/dqc_reference/reference_markers.fasta -out GCA_019118545.1_ASM1911854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:36:01,633] [INFO] Task succeeded: Blastn
[2023-06-28 17:36:01,639] [INFO] Selected 22 target genomes.
[2023-06-28 17:36:01,639] [INFO] Target genome list was writen to GCA_019118545.1_ASM1911854v1_genomic.fna/target_genomes.txt
[2023-06-28 17:36:01,641] [INFO] Task started: fastANI
[2023-06-28 17:36:01,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg8904f517-b2cc-4b5a-8744-61f898ed8790/GCA_019118545.1_ASM1911854v1_genomic.fna.gz --refList GCA_019118545.1_ASM1911854v1_genomic.fna/target_genomes.txt --output GCA_019118545.1_ASM1911854v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:36:14,296] [INFO] Task succeeded: fastANI
[2023-06-28 17:36:14,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10e6e960-11bd-480e-bdfd-02c6cf6607bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:36:14,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10e6e960-11bd-480e-bdfd-02c6cf6607bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:36:14,310] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:36:14,310] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:36:14,310] [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	78.6425	241	836	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	77.7094	149	836	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.6193	123	836	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	77.6023	123	836	95	below_threshold
Mediterraneibacter massiliensis	strain=Marseille-P2086	GCA_001487105.1	1720300	1720300	type	True	77.258	109	836	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	77.1632	98	836	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.0553	153	836	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	76.9372	63	836	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	76.8809	130	836	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	76.8628	131	836	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	76.8585	135	836	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	76.8106	133	836	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	76.8093	131	836	95	below_threshold
Muricomes intestini	strain=DSM 29489	GCA_004346165.1	1796634	1796634	type	True	76.6643	66	836	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.2048	61	836	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.195	61	836	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:36:14,312] [INFO] DFAST Taxonomy check result was written to GCA_019118545.1_ASM1911854v1_genomic.fna/tc_result.tsv
[2023-06-28 17:36:14,313] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:36:14,313] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:36:14,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10e6e960-11bd-480e-bdfd-02c6cf6607bb/dqc_reference/checkm_data
[2023-06-28 17:36:14,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:36:14,354] [INFO] Task started: CheckM
[2023-06-28 17:36:14,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019118545.1_ASM1911854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019118545.1_ASM1911854v1_genomic.fna/checkm_input GCA_019118545.1_ASM1911854v1_genomic.fna/checkm_result
[2023-06-28 17:36:42,025] [INFO] Task succeeded: CheckM
[2023-06-28 17:36:42,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 17:36:42,058] [INFO] ===== Completeness check finished =====
[2023-06-28 17:36:42,058] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:36:42,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019118545.1_ASM1911854v1_genomic.fna/markers.fasta)
[2023-06-28 17:36:42,059] [INFO] Task started: Blastn
[2023-06-28 17:36:42,059] [INFO] Running command: blastn -query GCA_019118545.1_ASM1911854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10e6e960-11bd-480e-bdfd-02c6cf6607bb/dqc_reference/reference_markers_gtdb.fasta -out GCA_019118545.1_ASM1911854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:36:43,202] [INFO] Task succeeded: Blastn
[2023-06-28 17:36:43,207] [INFO] Selected 12 target genomes.
[2023-06-28 17:36:43,207] [INFO] Target genome list was writen to GCA_019118545.1_ASM1911854v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:36:43,214] [INFO] Task started: fastANI
[2023-06-28 17:36:43,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg8904f517-b2cc-4b5a-8744-61f898ed8790/GCA_019118545.1_ASM1911854v1_genomic.fna.gz --refList GCA_019118545.1_ASM1911854v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019118545.1_ASM1911854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:36:50,021] [INFO] Task succeeded: fastANI
[2023-06-28 17:36:50,036] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:36:50,037] [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_019118545.1	s__Mediterraneibacter merdavium	100.0	830	836	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.49	99.49	0.84	0.84	2	conclusive
GCA_904418845.1	s__Mediterraneibacter sp904418845	85.5618	546	836	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_900761655.1	s__Mediterraneibacter sp900761655	83.7435	407	836	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_019117065.1	s__Mediterraneibacter pullicola	81.0978	430	836	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.71	99.71	0.95	0.95	2	-
GCF_002161355.1	s__Mediterraneibacter caccavium	80.0804	350	836	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.91	97.67	0.90	0.86	7	-
GCA_019120595.1	s__Mediterraneibacter tabaqchaliae	79.4173	292	836	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_019116185.1	s__Mediterraneibacter stercorigallinarum	78.8987	267	836	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_019112735.1	s__Mediterraneibacter guildfordensis	78.6532	266	836	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_019114745.1	s__Mediterraneibacter colneyensis	78.341	205	836	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_019120275.1	s__Mediterraneibacter excrementavium	78.3281	229	836	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	78.3161	232	836	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_019118885.1	s__Mediterraneibacter surreyensis	78.2748	266	836	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.86	98.12	0.80	0.76	3	-
--------------------------------------------------------------------------------
[2023-06-28 17:36:50,039] [INFO] GTDB search result was written to GCA_019118545.1_ASM1911854v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:36:50,040] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:36:50,044] [INFO] DFAST_QC result json was written to GCA_019118545.1_ASM1911854v1_genomic.fna/dqc_result.json
[2023-06-28 17:36:50,045] [INFO] DFAST_QC completed!
[2023-06-28 17:36:50,045] [INFO] Total running time: 0h0m57s