[2023-06-05 18:57:00,074] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:57:00,076] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:57:00,076] [INFO] DQC Reference Directory: /var/lib/cwl/stg116f67cd-76c1-4dce-9cf3-7ebbbdd4fb40/dqc_reference
[2023-06-05 18:57:01,494] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:57:01,495] [INFO] Task started: Prodigal
[2023-06-05 18:57:01,496] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c76bcb8-0e0d-4f4a-ad48-8771143d842e/GCA_934853085.1_MTG234_bin.44.fa_genomic.fna.gz | prodigal -d GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/cds.fna -a GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:57:07,589] [INFO] Task succeeded: Prodigal
[2023-06-05 18:57:07,590] [INFO] Task started: HMMsearch
[2023-06-05 18:57:07,590] [INFO] Running command: hmmsearch --tblout GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg116f67cd-76c1-4dce-9cf3-7ebbbdd4fb40/dqc_reference/reference_markers.hmm GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:57:07,960] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:57:07,962] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3c76bcb8-0e0d-4f4a-ad48-8771143d842e/GCA_934853085.1_MTG234_bin.44.fa_genomic.fna.gz]
[2023-06-05 18:57:07,995] [INFO] Query marker FASTA was written to GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/markers.fasta
[2023-06-05 18:57:07,996] [INFO] Task started: Blastn
[2023-06-05 18:57:07,996] [INFO] Running command: blastn -query GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg116f67cd-76c1-4dce-9cf3-7ebbbdd4fb40/dqc_reference/reference_markers.fasta -out GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:08,983] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:08,988] [INFO] Selected 19 target genomes.
[2023-06-05 18:57:08,988] [INFO] Target genome list was writen to GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/target_genomes.txt
[2023-06-05 18:57:08,989] [INFO] Task started: fastANI
[2023-06-05 18:57:08,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c76bcb8-0e0d-4f4a-ad48-8771143d842e/GCA_934853085.1_MTG234_bin.44.fa_genomic.fna.gz --refList GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/target_genomes.txt --output GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:57:27,621] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:27,622] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg116f67cd-76c1-4dce-9cf3-7ebbbdd4fb40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:57:27,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg116f67cd-76c1-4dce-9cf3-7ebbbdd4fb40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:57:27,630] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 18:57:27,630] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 18:57:27,630] [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
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	98.2243	559	594	95	conclusive
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.9213	191	594	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.8974	190	594	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.8805	192	594	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.6096	131	594	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	76.6956	79	594	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:57:27,633] [INFO] DFAST Taxonomy check result was written to GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/tc_result.tsv
[2023-06-05 18:57:27,634] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:57:27,634] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:57:27,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg116f67cd-76c1-4dce-9cf3-7ebbbdd4fb40/dqc_reference/checkm_data
[2023-06-05 18:57:27,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:57:27,668] [INFO] Task started: CheckM
[2023-06-05 18:57:27,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/checkm_input GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/checkm_result
[2023-06-05 18:57:52,558] [INFO] Task succeeded: CheckM
[2023-06-05 18:57:52,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:57:52,581] [INFO] ===== Completeness check finished =====
[2023-06-05 18:57:52,581] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:57:52,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/markers.fasta)
[2023-06-05 18:57:52,582] [INFO] Task started: Blastn
[2023-06-05 18:57:52,582] [INFO] Running command: blastn -query GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg116f67cd-76c1-4dce-9cf3-7ebbbdd4fb40/dqc_reference/reference_markers_gtdb.fasta -out GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:53,457] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:53,463] [INFO] Selected 19 target genomes.
[2023-06-05 18:57:53,463] [INFO] Target genome list was writen to GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:57:53,470] [INFO] Task started: fastANI
[2023-06-05 18:57:53,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c76bcb8-0e0d-4f4a-ad48-8771143d842e/GCA_934853085.1_MTG234_bin.44.fa_genomic.fna.gz --refList GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:58:04,164] [INFO] Task succeeded: fastANI
[2023-06-05 18:58:04,180] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:58:04,180] [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_000225345.1	s__Roseburia hominis	98.2243	559	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	conclusive
GCA_017937095.1	s__Roseburia sp017937095	79.3363	311	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483745.1	s__Roseburia sp003483745	77.9807	159	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCF_900537995.1	s__Roseburia intestinalis	77.9334	188	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	-
GCA_900753715.1	s__Roseburia sp900753715	77.6528	138	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	99.04	99.04	0.83	0.83	2	-
GCF_003470905.1	s__Roseburia sp003470905	77.6457	185	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCA_900548205.1	s__Roseburia sp900548205	77.3467	116	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	99.97	99.97	0.82	0.82	2	-
GCA_900550935.1	s__Roseburia sp900550935	77.3352	147	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.33	98.19	0.83	0.82	3	-
GCA_900542495.1	s__Roseburia sp900542495	77.1152	138	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.47	97.09	0.82	0.76	4	-
GCA_910587865.1	s__Roseburia sp910587865	77.1036	139	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363825.1	s__CAG-45 sp000438375	77.0559	112	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	98.60	98.28	0.92	0.87	6	-
--------------------------------------------------------------------------------
[2023-06-05 18:58:04,182] [INFO] GTDB search result was written to GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 18:58:04,183] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:58:04,186] [INFO] DFAST_QC result json was written to GCA_934853085.1_MTG234_bin.44.fa_genomic.fna/dqc_result.json
[2023-06-05 18:58:04,186] [INFO] DFAST_QC completed!
[2023-06-05 18:58:04,186] [INFO] Total running time: 0h1m4s