[2024-01-24 13:36:45,434] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,438] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6111712-64a2-41f7-8b96-1c60515bfc4e/dqc_reference
[2024-01-24 13:36:46,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,742] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,742] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d519300-be5b-4ce7-abaf-7c607feef39c/GCF_000155205.1_ASM15520v1_genomic.fna.gz | prodigal -d GCF_000155205.1_ASM15520v1_genomic.fna/cds.fna -a GCF_000155205.1_ASM15520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:53,042] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:53,042] [INFO] Task started: HMMsearch
[2024-01-24 13:36:53,043] [INFO] Running command: hmmsearch --tblout GCF_000155205.1_ASM15520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6111712-64a2-41f7-8b96-1c60515bfc4e/dqc_reference/reference_markers.hmm GCF_000155205.1_ASM15520v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:53,316] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:53,320] [INFO] Found 6/6 markers.
[2024-01-24 13:36:53,348] [INFO] Query marker FASTA was written to GCF_000155205.1_ASM15520v1_genomic.fna/markers.fasta
[2024-01-24 13:36:53,349] [INFO] Task started: Blastn
[2024-01-24 13:36:53,349] [INFO] Running command: blastn -query GCF_000155205.1_ASM15520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6111712-64a2-41f7-8b96-1c60515bfc4e/dqc_reference/reference_markers.fasta -out GCF_000155205.1_ASM15520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:54,004] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:54,007] [INFO] Selected 13 target genomes.
[2024-01-24 13:36:54,007] [INFO] Target genome list was writen to GCF_000155205.1_ASM15520v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:54,036] [INFO] Task started: fastANI
[2024-01-24 13:36:54,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d519300-be5b-4ce7-abaf-7c607feef39c/GCF_000155205.1_ASM15520v1_genomic.fna.gz --refList GCF_000155205.1_ASM15520v1_genomic.fna/target_genomes.txt --output GCF_000155205.1_ASM15520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:02,492] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:02,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6111712-64a2-41f7-8b96-1c60515bfc4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:02,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6111712-64a2-41f7-8b96-1c60515bfc4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:02,503] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:02,503] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:02,504] [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
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	100.0	885	887	95	conclusive
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	99.9668	878	887	95	conclusive
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	80.2693	197	887	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	79.1936	237	887	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	79.128	98	887	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	79.0326	173	887	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	78.9937	236	887	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	78.9186	236	887	95	below_threshold
Mediterraneibacter massiliensis	strain=Marseille-P2086	GCA_001487105.1	1720300	1720300	type	True	78.6288	154	887	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	78.4515	172	887	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	78.4163	163	887	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	78.3492	118	887	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:02,506] [INFO] DFAST Taxonomy check result was written to GCF_000155205.1_ASM15520v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:02,506] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:02,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:02,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6111712-64a2-41f7-8b96-1c60515bfc4e/dqc_reference/checkm_data
[2024-01-24 13:37:02,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:02,541] [INFO] Task started: CheckM
[2024-01-24 13:37:02,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000155205.1_ASM15520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000155205.1_ASM15520v1_genomic.fna/checkm_input GCF_000155205.1_ASM15520v1_genomic.fna/checkm_result
[2024-01-24 13:37:29,557] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:29,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:29,579] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:29,580] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:29,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000155205.1_ASM15520v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:29,581] [INFO] Task started: Blastn
[2024-01-24 13:37:29,581] [INFO] Running command: blastn -query GCF_000155205.1_ASM15520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6111712-64a2-41f7-8b96-1c60515bfc4e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000155205.1_ASM15520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:30,705] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:30,709] [INFO] Selected 22 target genomes.
[2024-01-24 13:37:30,709] [INFO] Target genome list was writen to GCF_000155205.1_ASM15520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:30,721] [INFO] Task started: fastANI
[2024-01-24 13:37:30,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d519300-be5b-4ce7-abaf-7c607feef39c/GCF_000155205.1_ASM15520v1_genomic.fna.gz --refList GCF_000155205.1_ASM15520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000155205.1_ASM15520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:44,617] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:44,634] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:44,634] [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_000155205.1	s__Mediterraneibacter lactaris	100.0	885	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	conclusive
GCA_001312505.1	s__Mediterraneibacter faecis	80.8238	334	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.72	95.03	0.76	0.67	61	-
GCF_003574295.1	s__Mediterraneibacter_A butyricigenes	80.3468	194	887	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_001404875.1	s__Dorea_A longicatena_B	79.917	190	887	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	-
GCA_003480425.1	s__Schaedlerella sp900066545	79.6816	207	887	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_008121495.1	s__Ruminococcus_B gnavus	79.2698	238	887	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_003435815.1	s__CAG-317 sp000433215	79.251	185	887	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	-
GCF_002159505.1	s__Mediterraneibacter ornithocaccae	78.596	175	887	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_004556565.1	s__Schaedlerella sp004556565	78.4512	137	887	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_900120155.1	s__Mediterraneibacter sp900120155	78.2847	157	887	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_002160525.1	s__Mediterraneibacter cottocaccae	78.2181	183	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.81	98.78	0.88	0.86	3	-
GCA_900544395.1	s__Ruminococcus_B sp900544395	78.1175	174	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	99.21	99.21	0.88	0.88	2	-
GCA_900550865.1	s__Dorea_A sp900550865	77.8935	155	887	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_904377845.1	s__Mediterraneibacter sp904377845	77.749	173	887	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_019119265.1	s__Mediterraneibacter intestinigallinarum	77.7483	158	887	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_019119995.1	s__Mediterraneibacter faecavium	77.7366	168	887	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_905209865.1	s__Mediterraneibacter sp900752395	77.6772	149	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.94	99.94	0.94	0.94	2	-
GCA_019119745.1	s__Mediterraneibacter gallistercoris	77.6272	140	887	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_019120275.1	s__Mediterraneibacter excrementavium	77.5966	137	887	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_019115385.1	s__Mediterraneibacter avicola	77.534	148	887	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_019119675.1	s__Mediterraneibacter faecipullorum	77.301	182	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:44,636] [INFO] GTDB search result was written to GCF_000155205.1_ASM15520v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:44,637] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:44,649] [INFO] DFAST_QC result json was written to GCF_000155205.1_ASM15520v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:44,650] [INFO] DFAST_QC completed!
[2024-01-24 13:37:44,650] [INFO] Total running time: 0h0m59s