[2024-01-24 13:49:55,377] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,378] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f7c0027-79a2-45f2-8a45-d492bf84ede4/dqc_reference
[2024-01-24 13:49:56,772] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,772] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,773] [INFO] Running command: gunzip -c /var/lib/cwl/stg4379ccec-1c62-416e-b866-ecfd2534586e/GCF_014287355.1_ASM1428735v1_genomic.fna.gz | prodigal -d GCF_014287355.1_ASM1428735v1_genomic.fna/cds.fna -a GCF_014287355.1_ASM1428735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:05,328] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:05,328] [INFO] Task started: HMMsearch
[2024-01-24 13:50:05,328] [INFO] Running command: hmmsearch --tblout GCF_014287355.1_ASM1428735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f7c0027-79a2-45f2-8a45-d492bf84ede4/dqc_reference/reference_markers.hmm GCF_014287355.1_ASM1428735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:05,611] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:05,612] [INFO] Found 6/6 markers.
[2024-01-24 13:50:05,642] [INFO] Query marker FASTA was written to GCF_014287355.1_ASM1428735v1_genomic.fna/markers.fasta
[2024-01-24 13:50:05,642] [INFO] Task started: Blastn
[2024-01-24 13:50:05,643] [INFO] Running command: blastn -query GCF_014287355.1_ASM1428735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f7c0027-79a2-45f2-8a45-d492bf84ede4/dqc_reference/reference_markers.fasta -out GCF_014287355.1_ASM1428735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:06,402] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:06,406] [INFO] Selected 29 target genomes.
[2024-01-24 13:50:06,406] [INFO] Target genome list was writen to GCF_014287355.1_ASM1428735v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:06,413] [INFO] Task started: fastANI
[2024-01-24 13:50:06,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg4379ccec-1c62-416e-b866-ecfd2534586e/GCF_014287355.1_ASM1428735v1_genomic.fna.gz --refList GCF_014287355.1_ASM1428735v1_genomic.fna/target_genomes.txt --output GCF_014287355.1_ASM1428735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:22,033] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:22,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f7c0027-79a2-45f2-8a45-d492bf84ede4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:22,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f7c0027-79a2-45f2-8a45-d492bf84ede4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:22,055] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:22,056] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:22,056] [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
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	84.0284	270	1151	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	83.5218	243	1151	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	83.4775	211	1151	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	81.5482	217	1151	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	81.3605	95	1151	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	81.3146	213	1151	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	81.2641	213	1151	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	81.2284	96	1151	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	81.0764	210	1151	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	80.7722	158	1151	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	80.7672	210	1151	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	80.7417	91	1151	95	below_threshold
Luxibacter massiliensis	strain=Marseille-P5551	GCA_900604355.1	2219695	2219695	type	True	80.602	141	1151	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	80.0332	197	1151	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.9622	207	1151	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	79.3742	131	1151	95	below_threshold
Hespellia stercorisuis	strain=DSM 15480	GCA_900142165.1	180311	180311	type	True	79.3461	126	1151	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	79.3396	151	1151	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	78.5781	99	1151	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	78.5275	123	1151	95	below_threshold
Anaerostipes faecalis	strain=AGMB03513	GCA_018982945.1	2738446	2738446	type	True	78.3566	78	1151	95	below_threshold
Mediterraneibacter massiliensis	strain=Marseille-P2086	GCA_001487105.1	1720300	1720300	type	True	78.1308	133	1151	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	77.8925	118	1151	95	below_threshold
Muricomes intestini	strain=DSM 29489	GCA_004346165.1	1796634	1796634	type	True	77.7929	115	1151	95	below_threshold
Frisingicoccus caecimuris	strain=DSM 28559	GCA_024622585.1	1796636	1796636	type	True	77.5622	67	1151	95	below_threshold
Frisingicoccus caecimuris	strain=DSM 28559	GCA_004340975.1	1796636	1796636	type	True	77.547	67	1151	95	below_threshold
Lachnotalea glycerini	strain=DSM 28816	GCA_003201285.1	1763509	1763509	type	True	76.601	52	1151	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:22,057] [INFO] DFAST Taxonomy check result was written to GCF_014287355.1_ASM1428735v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:22,058] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:22,058] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:22,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f7c0027-79a2-45f2-8a45-d492bf84ede4/dqc_reference/checkm_data
[2024-01-24 13:50:22,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:22,095] [INFO] Task started: CheckM
[2024-01-24 13:50:22,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287355.1_ASM1428735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287355.1_ASM1428735v1_genomic.fna/checkm_input GCF_014287355.1_ASM1428735v1_genomic.fna/checkm_result
[2024-01-24 13:50:52,588] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:52,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:52,606] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:52,607] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:52,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287355.1_ASM1428735v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:52,608] [INFO] Task started: Blastn
[2024-01-24 13:50:52,608] [INFO] Running command: blastn -query GCF_014287355.1_ASM1428735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f7c0027-79a2-45f2-8a45-d492bf84ede4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287355.1_ASM1428735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:53,643] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:53,647] [INFO] Selected 20 target genomes.
[2024-01-24 13:50:53,647] [INFO] Target genome list was writen to GCF_014287355.1_ASM1428735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:53,698] [INFO] Task started: fastANI
[2024-01-24 13:50:53,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg4379ccec-1c62-416e-b866-ecfd2534586e/GCF_014287355.1_ASM1428735v1_genomic.fna.gz --refList GCF_014287355.1_ASM1428735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287355.1_ASM1428735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:04,529] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:04,549] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:04,549] [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_003480425.1	s__Schaedlerella sp900066545	98.0776	868	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.16	96.52	0.81	0.77	11	conclusive
GCF_000169235.1	s__Dorea formicigenerans	84.0028	258	1151	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_001312505.1	s__Mediterraneibacter faecis	83.5285	365	1151	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_003435815.1	s__CAG-317 sp000433215	82.3321	204	1151	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_008121495.1	s__Ruminococcus_B gnavus	81.5938	218	1151	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_000155205.1	s__Mediterraneibacter lactaris	80.0242	199	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCA_900544395.1	s__Ruminococcus_B sp900544395	79.7433	172	1151	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	-
GCF_001940315.1	s__Anaerostipes sp001940315	79.5198	82	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.20	99.20	0.89	0.89	2	-
GCF_000153925.1	s__Mediterraneibacter torques	79.4501	152	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.42	99.19	0.88	0.82	25	-
GCA_905203555.1	s__Schaedlerella sp905203555	79.3759	200	1151	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_900142165.1	s__Hespellia stercorisuis	79.3373	127	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hespellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320245.1	s__Schaedlerella sp002320245	79.2136	248	1151	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_900765975.1	s__Schaedlerella sp900765975	78.7578	189	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.94	99.94	0.80	0.80	2	-
GCF_015560805.1	s__Schaedlerella glycyrrhizinilytica_A	78.3634	175	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.33	97.63	0.90	0.83	10	-
GCF_001028025.1	s__Muricomes fissicatena_A	78.1757	126	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	99.01	99.01	0.90	0.90	3	-
GCA_900551895.1	s__Faecalimonas sp900551895	77.9219	78	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.69	98.58	0.83	0.80	3	-
GCA_900550865.1	s__Dorea_A sp900550865	77.7846	150	1151	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_019112765.1	s__Mediterraneibacter norwichensis	76.9565	79	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.85	97.86	0.81	0.76	3	-
GCA_905201915.1	s__Blautia sp900555025	76.7758	92	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.26	99.26	0.76	0.76	2	-
GCA_019116185.1	s__Mediterraneibacter stercorigallinarum	76.6356	58	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.63	98.63	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:04,551] [INFO] GTDB search result was written to GCF_014287355.1_ASM1428735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:04,551] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:04,556] [INFO] DFAST_QC result json was written to GCF_014287355.1_ASM1428735v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:04,556] [INFO] DFAST_QC completed!
[2024-01-24 13:51:04,556] [INFO] Total running time: 0h1m9s