[2024-01-24 14:14:20,254] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,256] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,257] [INFO] DQC Reference Directory: /var/lib/cwl/stg2017bc16-e9d3-4cf9-bb8e-d95c16183911/dqc_reference
[2024-01-24 14:14:21,557] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,558] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,559] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4e3675d-25fc-46f1-a1df-11cf2099d315/GCF_900312975.1_PRJEB24953_genomic.fna.gz | prodigal -d GCF_900312975.1_PRJEB24953_genomic.fna/cds.fna -a GCF_900312975.1_PRJEB24953_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:28,967] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:28,967] [INFO] Task started: HMMsearch
[2024-01-24 14:14:28,967] [INFO] Running command: hmmsearch --tblout GCF_900312975.1_PRJEB24953_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2017bc16-e9d3-4cf9-bb8e-d95c16183911/dqc_reference/reference_markers.hmm GCF_900312975.1_PRJEB24953_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:29,236] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:29,241] [INFO] Found 6/6 markers.
[2024-01-24 14:14:29,275] [INFO] Query marker FASTA was written to GCF_900312975.1_PRJEB24953_genomic.fna/markers.fasta
[2024-01-24 14:14:29,276] [INFO] Task started: Blastn
[2024-01-24 14:14:29,276] [INFO] Running command: blastn -query GCF_900312975.1_PRJEB24953_genomic.fna/markers.fasta -db /var/lib/cwl/stg2017bc16-e9d3-4cf9-bb8e-d95c16183911/dqc_reference/reference_markers.fasta -out GCF_900312975.1_PRJEB24953_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:29,962] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:29,966] [INFO] Selected 25 target genomes.
[2024-01-24 14:14:29,966] [INFO] Target genome list was writen to GCF_900312975.1_PRJEB24953_genomic.fna/target_genomes.txt
[2024-01-24 14:14:30,104] [INFO] Task started: fastANI
[2024-01-24 14:14:30,105] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4e3675d-25fc-46f1-a1df-11cf2099d315/GCF_900312975.1_PRJEB24953_genomic.fna.gz --refList GCF_900312975.1_PRJEB24953_genomic.fna/target_genomes.txt --output GCF_900312975.1_PRJEB24953_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:47,665] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:47,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2017bc16-e9d3-4cf9-bb8e-d95c16183911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:47,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2017bc16-e9d3-4cf9-bb8e-d95c16183911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:47,683] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:47,683] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:47,684] [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	100.0	923	923	95	conclusive
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	81.078	294	923	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	80.1589	84	923	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	79.2611	93	923	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	79.1947	82	923	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	78.8341	87	923	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	78.8225	107	923	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	78.7029	79	923	95	below_threshold
Suipraeoptans intestinalis	strain=68-1-5	GCA_009696485.1	2606628	2606628	type	True	78.6996	122	923	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	78.6819	84	923	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	78.5657	95	923	95	below_threshold
Bariatricus massiliensis	strain=AT12	GCA_900086725.1	1745713	1745713	type	True	78.5657	89	923	95	below_threshold
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	78.5553	175	923	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	78.4694	236	923	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	78.4176	241	923	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	78.1081	128	923	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	78.0184	184	923	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	77.9754	82	923	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	77.7709	116	923	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	77.5716	106	923	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.3407	105	923	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	77.1823	80	923	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	77.0738	83	923	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:47,685] [INFO] DFAST Taxonomy check result was written to GCF_900312975.1_PRJEB24953_genomic.fna/tc_result.tsv
[2024-01-24 14:14:47,686] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:47,686] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:47,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2017bc16-e9d3-4cf9-bb8e-d95c16183911/dqc_reference/checkm_data
[2024-01-24 14:14:47,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:47,715] [INFO] Task started: CheckM
[2024-01-24 14:14:47,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900312975.1_PRJEB24953_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900312975.1_PRJEB24953_genomic.fna/checkm_input GCF_900312975.1_PRJEB24953_genomic.fna/checkm_result
[2024-01-24 14:15:14,773] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:14,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:14,790] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:14,791] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:14,791] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900312975.1_PRJEB24953_genomic.fna/markers.fasta)
[2024-01-24 14:15:14,791] [INFO] Task started: Blastn
[2024-01-24 14:15:14,791] [INFO] Running command: blastn -query GCF_900312975.1_PRJEB24953_genomic.fna/markers.fasta -db /var/lib/cwl/stg2017bc16-e9d3-4cf9-bb8e-d95c16183911/dqc_reference/reference_markers_gtdb.fasta -out GCF_900312975.1_PRJEB24953_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:15,842] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:15,846] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:15,846] [INFO] Target genome list was writen to GCF_900312975.1_PRJEB24953_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:15,865] [INFO] Task started: fastANI
[2024-01-24 14:15:15,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4e3675d-25fc-46f1-a1df-11cf2099d315/GCF_900312975.1_PRJEB24953_genomic.fna.gz --refList GCF_900312975.1_PRJEB24953_genomic.fna/target_genomes_gtdb.txt --output GCF_900312975.1_PRJEB24953_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:26,775] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:26,789] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:26,790] [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_900312975.1	s__Massilistercora timonensis	100.0	923	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Massilistercora	95.0	95.86	95.52	0.90	0.88	4	conclusive
GCF_001754075.1	s__Merdimonas faecis	81.0597	294	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	98.52	97.96	0.90	0.84	10	-
GCF_016902415.1	s__Merdimonas massiliensis	80.8219	318	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	97.93	97.91	0.86	0.83	3	-
GCA_019114065.1	s__Massilistercora gallistercoris	80.7318	396	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Massilistercora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902406105.1	s__Massilistercora sp902406105	80.3524	411	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Massilistercora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160985.1	s__Lachnoclostridium_B stercoravium	80.0674	304	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	98.37	98.26	0.93	0.92	3	-
GCF_000765215.1	s__Lachnoclostridium_B sp000765215	79.9575	283	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	98.26	97.36	0.89	0.84	10	-
GCF_003435815.1	s__CAG-317 sp000433215	78.3315	135	923	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	-
GCA_910574715.1	s__Sporofaciens sp910574715	78.1212	214	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.89	98.89	0.95	0.95	2	-
GCA_010206225.2	s__MD308 sp010206225	77.9333	127	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	98.71	98.71	0.87	0.87	2	-
GCA_009911175.1	s__Schaedlerella sp009911175	77.8722	165	923	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_000509125.1	s__Clostridium_AP sp000509125	77.7947	209	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP	95.0	99.12	98.62	0.95	0.91	5	-
GCA_000433535.1	s__CAG-317 sp000433535	77.6399	125	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.49	98.19	0.84	0.83	3	-
GCA_910575475.1	s__Schaedlerella sp910575475	77.5518	175	923	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_910587575.1	s__Sporofaciens sp910587575	77.1572	179	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715565.1	s__Ventrimonas merdavium	77.0358	109	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
GCA_904419285.1	s__Mediterraneibacter caccogallinarum	77.011	132	923	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.44	97.89	0.90	0.83	10	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:26,792] [INFO] GTDB search result was written to GCF_900312975.1_PRJEB24953_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:26,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:26,798] [INFO] DFAST_QC result json was written to GCF_900312975.1_PRJEB24953_genomic.fna/dqc_result.json
[2024-01-24 14:15:26,798] [INFO] DFAST_QC completed!
[2024-01-24 14:15:26,798] [INFO] Total running time: 0h1m7s