[2024-01-24 11:35:22,542] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:22,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:22,544] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8ea8b42-d3df-49b4-a660-dfcf729882dd/dqc_reference
[2024-01-24 11:35:26,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,240] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,240] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf8af379-4409-4381-bfde-11eb283682dd/GCF_014202115.1_ASM1420211v1_genomic.fna.gz | prodigal -d GCF_014202115.1_ASM1420211v1_genomic.fna/cds.fna -a GCF_014202115.1_ASM1420211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:35,950] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:35,951] [INFO] Task started: HMMsearch
[2024-01-24 11:35:35,951] [INFO] Running command: hmmsearch --tblout GCF_014202115.1_ASM1420211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8ea8b42-d3df-49b4-a660-dfcf729882dd/dqc_reference/reference_markers.hmm GCF_014202115.1_ASM1420211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:36,283] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:36,285] [INFO] Found 6/6 markers.
[2024-01-24 11:35:36,318] [INFO] Query marker FASTA was written to GCF_014202115.1_ASM1420211v1_genomic.fna/markers.fasta
[2024-01-24 11:35:36,318] [INFO] Task started: Blastn
[2024-01-24 11:35:36,318] [INFO] Running command: blastn -query GCF_014202115.1_ASM1420211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8ea8b42-d3df-49b4-a660-dfcf729882dd/dqc_reference/reference_markers.fasta -out GCF_014202115.1_ASM1420211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:36,965] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:36,969] [INFO] Selected 26 target genomes.
[2024-01-24 11:35:36,969] [INFO] Target genome list was writen to GCF_014202115.1_ASM1420211v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:36,988] [INFO] Task started: fastANI
[2024-01-24 11:35:36,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf8af379-4409-4381-bfde-11eb283682dd/GCF_014202115.1_ASM1420211v1_genomic.fna.gz --refList GCF_014202115.1_ASM1420211v1_genomic.fna/target_genomes.txt --output GCF_014202115.1_ASM1420211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:53,063] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:53,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8ea8b42-d3df-49b4-a660-dfcf729882dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:53,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8ea8b42-d3df-49b4-a660-dfcf729882dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:53,075] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:53,076] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:53,076] [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
Catenibacillus scindens	strain=DSM 106146	GCA_014202115.1	673271	673271	type	True	100.0	1263	1263	95	conclusive
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	79.6342	51	1263	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	78.7681	51	1263	95	below_threshold
Frisingicoccus caecimuris	strain=DSM 28559	GCA_024622585.1	1796636	1796636	type	True	78.3044	89	1263	95	below_threshold
Frisingicoccus caecimuris	strain=DSM 28559	GCA_004340975.1	1796636	1796636	type	True	78.2378	89	1263	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	77.3864	85	1263	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.7525	51	1263	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.6439	53	1263	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.6087	55	1263	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	76.5792	52	1263	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	76.4233	56	1263	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	76.389	57	1263	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	76.3058	56	1263	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:53,078] [INFO] DFAST Taxonomy check result was written to GCF_014202115.1_ASM1420211v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:53,078] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:53,078] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:53,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8ea8b42-d3df-49b4-a660-dfcf729882dd/dqc_reference/checkm_data
[2024-01-24 11:35:53,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:53,117] [INFO] Task started: CheckM
[2024-01-24 11:35:53,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202115.1_ASM1420211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202115.1_ASM1420211v1_genomic.fna/checkm_input GCF_014202115.1_ASM1420211v1_genomic.fna/checkm_result
[2024-01-24 11:36:27,895] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:27,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:27,918] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:27,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:27,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202115.1_ASM1420211v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:27,920] [INFO] Task started: Blastn
[2024-01-24 11:36:27,920] [INFO] Running command: blastn -query GCF_014202115.1_ASM1420211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8ea8b42-d3df-49b4-a660-dfcf729882dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202115.1_ASM1420211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:29,000] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:29,004] [INFO] Selected 22 target genomes.
[2024-01-24 11:36:29,004] [INFO] Target genome list was writen to GCF_014202115.1_ASM1420211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:29,055] [INFO] Task started: fastANI
[2024-01-24 11:36:29,055] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf8af379-4409-4381-bfde-11eb283682dd/GCF_014202115.1_ASM1420211v1_genomic.fna.gz --refList GCF_014202115.1_ASM1420211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202115.1_ASM1420211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:42,630] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:42,648] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:42,648] [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_014202115.1	s__Catenibacillus scindens	100.0	1263	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catenibacillus	95.0	98.94	98.94	0.95	0.95	2	conclusive
GCF_002160765.1	s__Merdisoma faecalis	80.1647	75	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.59	98.32	0.91	0.81	8	-
GCA_018711005.1	s__Catenibacillus faecigallinarum	79.1688	405	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catenibacillus	95.0	99.82	99.82	0.94	0.94	2	-
GCA_018713145.1	s__Catenibacillus faecavium	79.1004	344	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catenibacillus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_002160825.1	s__Merdisoma sp002160825	79.0196	57	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.04	99.04	0.92	0.92	2	-
GCA_902362725.1	s__Merdisoma sp900066385	78.3109	61	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.97	97.93	0.91	0.83	3	-
GCA_003481005.1	s__Eisenbergiella sp900066775	78.1011	61	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	97.95	96.96	0.88	0.78	15	-
GCA_018716485.1	s__Scybalocola faecipullorum	77.9774	99	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scybalocola	95.0	99.49	99.00	0.90	0.85	3	-
GCA_018369015.1	s__Catenibacillus sp018369015	77.9619	261	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363555.1	s__Catenibacillus sp902363555	77.677	266	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905199445.1	s__Catenibacillus sp900553975	77.5678	167	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catenibacillus	95.0	99.69	99.69	0.90	0.90	2	-
GCF_014287615.1	s__Blautia sp001304935	77.5578	69	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.32	98.73	0.92	0.87	9	-
GCA_900757195.1	s__Frisingicoccus sp900757195	76.698	64	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.09	99.09	0.92	0.92	2	-
GCA_019116385.1	s__Blautia_A faecigallinarum	76.4622	62	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904397815.1	s__Paralachnospira_A sangeri	76.0647	70	1263	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:42,650] [INFO] GTDB search result was written to GCF_014202115.1_ASM1420211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:42,651] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:42,654] [INFO] DFAST_QC result json was written to GCF_014202115.1_ASM1420211v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:42,655] [INFO] DFAST_QC completed!
[2024-01-24 11:36:42,655] [INFO] Total running time: 0h1m20s