[2023-06-05 13:29:56,960] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:29:56,963] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:29:56,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f7d8828-7f4c-4c5e-b03e-51c4812ef3ec/dqc_reference
[2023-06-05 13:29:58,509] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:29:58,510] [INFO] Task started: Prodigal
[2023-06-05 13:29:58,510] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ea58144-802d-4036-b254-18369de7ae87/GCA_934154365.1_ERR7737973_bin.109_genomic.fna.gz | prodigal -d GCA_934154365.1_ERR7737973_bin.109_genomic.fna/cds.fna -a GCA_934154365.1_ERR7737973_bin.109_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:30:01,380] [INFO] Task succeeded: Prodigal
[2023-06-05 13:30:01,381] [INFO] Task started: HMMsearch
[2023-06-05 13:30:01,381] [INFO] Running command: hmmsearch --tblout GCA_934154365.1_ERR7737973_bin.109_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f7d8828-7f4c-4c5e-b03e-51c4812ef3ec/dqc_reference/reference_markers.hmm GCA_934154365.1_ERR7737973_bin.109_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:30:01,559] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:30:01,561] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5ea58144-802d-4036-b254-18369de7ae87/GCA_934154365.1_ERR7737973_bin.109_genomic.fna.gz]
[2023-06-05 13:30:01,581] [INFO] Query marker FASTA was written to GCA_934154365.1_ERR7737973_bin.109_genomic.fna/markers.fasta
[2023-06-05 13:30:01,581] [INFO] Task started: Blastn
[2023-06-05 13:30:01,581] [INFO] Running command: blastn -query GCA_934154365.1_ERR7737973_bin.109_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f7d8828-7f4c-4c5e-b03e-51c4812ef3ec/dqc_reference/reference_markers.fasta -out GCA_934154365.1_ERR7737973_bin.109_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:30:02,148] [INFO] Task succeeded: Blastn
[2023-06-05 13:30:02,152] [INFO] Selected 22 target genomes.
[2023-06-05 13:30:02,152] [INFO] Target genome list was writen to GCA_934154365.1_ERR7737973_bin.109_genomic.fna/target_genomes.txt
[2023-06-05 13:30:02,155] [INFO] Task started: fastANI
[2023-06-05 13:30:02,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea58144-802d-4036-b254-18369de7ae87/GCA_934154365.1_ERR7737973_bin.109_genomic.fna.gz --refList GCA_934154365.1_ERR7737973_bin.109_genomic.fna/target_genomes.txt --output GCA_934154365.1_ERR7737973_bin.109_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:30:13,382] [INFO] Task succeeded: fastANI
[2023-06-05 13:30:13,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f7d8828-7f4c-4c5e-b03e-51c4812ef3ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:30:13,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f7d8828-7f4c-4c5e-b03e-51c4812ef3ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:30:13,389] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:30:13,389] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 13:30:13,390] [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
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	75.0766	54	509	95	below_threshold
Romboutsia lituseburensis	strain=DSM 797	GCA_900103615.1	1537	1537	type	True	74.9009	53	509	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	74.8978	51	509	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	74.8968	52	509	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:30:13,397] [INFO] DFAST Taxonomy check result was written to GCA_934154365.1_ERR7737973_bin.109_genomic.fna/tc_result.tsv
[2023-06-05 13:30:13,398] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:30:13,398] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:30:13,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f7d8828-7f4c-4c5e-b03e-51c4812ef3ec/dqc_reference/checkm_data
[2023-06-05 13:30:13,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:30:13,420] [INFO] Task started: CheckM
[2023-06-05 13:30:13,420] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934154365.1_ERR7737973_bin.109_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934154365.1_ERR7737973_bin.109_genomic.fna/checkm_input GCA_934154365.1_ERR7737973_bin.109_genomic.fna/checkm_result
[2023-06-05 13:30:29,733] [INFO] Task succeeded: CheckM
[2023-06-05 13:30:29,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:30:29,751] [INFO] ===== Completeness check finished =====
[2023-06-05 13:30:29,751] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:30:29,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934154365.1_ERR7737973_bin.109_genomic.fna/markers.fasta)
[2023-06-05 13:30:29,751] [INFO] Task started: Blastn
[2023-06-05 13:30:29,751] [INFO] Running command: blastn -query GCA_934154365.1_ERR7737973_bin.109_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f7d8828-7f4c-4c5e-b03e-51c4812ef3ec/dqc_reference/reference_markers_gtdb.fasta -out GCA_934154365.1_ERR7737973_bin.109_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:30:30,472] [INFO] Task succeeded: Blastn
[2023-06-05 13:30:30,475] [INFO] Selected 6 target genomes.
[2023-06-05 13:30:30,476] [INFO] Target genome list was writen to GCA_934154365.1_ERR7737973_bin.109_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:30:30,477] [INFO] Task started: fastANI
[2023-06-05 13:30:30,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea58144-802d-4036-b254-18369de7ae87/GCA_934154365.1_ERR7737973_bin.109_genomic.fna.gz --refList GCA_934154365.1_ERR7737973_bin.109_genomic.fna/target_genomes_gtdb.txt --output GCA_934154365.1_ERR7737973_bin.109_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:30:32,849] [INFO] Task succeeded: fastANI
[2023-06-05 13:30:32,855] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 13:30:32,856] [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_900552555.1	s__CAG-269 sp900552555	89.9261	369	509	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001916065.1	s__CAG-269 sp001916065	89.9117	352	509	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.24	97.60	0.86	0.82	5	-
GCA_900753165.1	s__CAG-269 sp900753165	89.191	295	509	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.62	99.62	0.76	0.76	2	-
GCA_900551615.1	s__CAG-269 sp900551615	85.959	336	509	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.20	98.20	0.87	0.87	2	-
GCA_000438255.1	s__CAG-269 sp000438255	85.8419	320	509	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.47	98.35	0.85	0.83	3	-
GCA_001916005.1	s__CAG-269 sp001916005	82.1379	282	509	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	96.70	96.22	0.72	0.66	3	-
--------------------------------------------------------------------------------
[2023-06-05 13:30:32,858] [INFO] GTDB search result was written to GCA_934154365.1_ERR7737973_bin.109_genomic.fna/result_gtdb.tsv
[2023-06-05 13:30:32,858] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:30:32,861] [INFO] DFAST_QC result json was written to GCA_934154365.1_ERR7737973_bin.109_genomic.fna/dqc_result.json
[2023-06-05 13:30:32,862] [INFO] DFAST_QC completed!
[2023-06-05 13:30:32,862] [INFO] Total running time: 0h0m36s