[2023-06-08 00:03:33,744] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:03:33,746] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:03:33,747] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1c7b64e-52d7-461f-8c9c-c7762e40c3f5/dqc_reference
[2023-06-08 00:03:35,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:03:35,363] [INFO] Task started: Prodigal
[2023-06-08 00:03:35,363] [INFO] Running command: gunzip -c /var/lib/cwl/stg658c4006-4eb6-4ba2-a1ab-5e273e8e1e7f/GCA_945898065.1_MsH-30apr19-344_genomic.fna.gz | prodigal -d GCA_945898065.1_MsH-30apr19-344_genomic.fna/cds.fna -a GCA_945898065.1_MsH-30apr19-344_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:03:38,634] [INFO] Task succeeded: Prodigal
[2023-06-08 00:03:38,634] [INFO] Task started: HMMsearch
[2023-06-08 00:03:38,634] [INFO] Running command: hmmsearch --tblout GCA_945898065.1_MsH-30apr19-344_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1c7b64e-52d7-461f-8c9c-c7762e40c3f5/dqc_reference/reference_markers.hmm GCA_945898065.1_MsH-30apr19-344_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:03:38,839] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:03:38,840] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg658c4006-4eb6-4ba2-a1ab-5e273e8e1e7f/GCA_945898065.1_MsH-30apr19-344_genomic.fna.gz]
[2023-06-08 00:03:38,860] [INFO] Query marker FASTA was written to GCA_945898065.1_MsH-30apr19-344_genomic.fna/markers.fasta
[2023-06-08 00:03:38,861] [INFO] Task started: Blastn
[2023-06-08 00:03:38,861] [INFO] Running command: blastn -query GCA_945898065.1_MsH-30apr19-344_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1c7b64e-52d7-461f-8c9c-c7762e40c3f5/dqc_reference/reference_markers.fasta -out GCA_945898065.1_MsH-30apr19-344_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:03:39,359] [INFO] Task succeeded: Blastn
[2023-06-08 00:03:39,366] [INFO] Selected 14 target genomes.
[2023-06-08 00:03:39,367] [INFO] Target genome list was writen to GCA_945898065.1_MsH-30apr19-344_genomic.fna/target_genomes.txt
[2023-06-08 00:03:39,370] [INFO] Task started: fastANI
[2023-06-08 00:03:39,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg658c4006-4eb6-4ba2-a1ab-5e273e8e1e7f/GCA_945898065.1_MsH-30apr19-344_genomic.fna.gz --refList GCA_945898065.1_MsH-30apr19-344_genomic.fna/target_genomes.txt --output GCA_945898065.1_MsH-30apr19-344_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:03:43,472] [INFO] Task succeeded: fastANI
[2023-06-08 00:03:43,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1c7b64e-52d7-461f-8c9c-c7762e40c3f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:03:43,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1c7b64e-52d7-461f-8c9c-c7762e40c3f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:03:43,474] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:03:43,474] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 00:03:43,474] [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
--------------------------------------------------------------------------------
[2023-06-08 00:03:43,476] [INFO] DFAST Taxonomy check result was written to GCA_945898065.1_MsH-30apr19-344_genomic.fna/tc_result.tsv
[2023-06-08 00:03:43,477] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:03:43,477] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:03:43,477] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1c7b64e-52d7-461f-8c9c-c7762e40c3f5/dqc_reference/checkm_data
[2023-06-08 00:03:43,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:03:43,497] [INFO] Task started: CheckM
[2023-06-08 00:03:43,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945898065.1_MsH-30apr19-344_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945898065.1_MsH-30apr19-344_genomic.fna/checkm_input GCA_945898065.1_MsH-30apr19-344_genomic.fna/checkm_result
[2023-06-08 00:04:01,666] [INFO] Task succeeded: CheckM
[2023-06-08 00:04:01,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:04:01,729] [INFO] ===== Completeness check finished =====
[2023-06-08 00:04:01,729] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:04:01,730] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945898065.1_MsH-30apr19-344_genomic.fna/markers.fasta)
[2023-06-08 00:04:01,730] [INFO] Task started: Blastn
[2023-06-08 00:04:01,730] [INFO] Running command: blastn -query GCA_945898065.1_MsH-30apr19-344_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1c7b64e-52d7-461f-8c9c-c7762e40c3f5/dqc_reference/reference_markers_gtdb.fasta -out GCA_945898065.1_MsH-30apr19-344_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:04:02,170] [INFO] Task succeeded: Blastn
[2023-06-08 00:04:02,183] [INFO] Selected 14 target genomes.
[2023-06-08 00:04:02,183] [INFO] Target genome list was writen to GCA_945898065.1_MsH-30apr19-344_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:04:02,187] [INFO] Task started: fastANI
[2023-06-08 00:04:02,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg658c4006-4eb6-4ba2-a1ab-5e273e8e1e7f/GCA_945898065.1_MsH-30apr19-344_genomic.fna.gz --refList GCA_945898065.1_MsH-30apr19-344_genomic.fna/target_genomes_gtdb.txt --output GCA_945898065.1_MsH-30apr19-344_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:04:05,277] [INFO] Task succeeded: fastANI
[2023-06-08 00:04:05,288] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 00:04:05,288] [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_903932885.1	s__Planktophila sp903932885	88.0057	183	431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.32	98.32	0.73	0.73	2	-
GCA_009705025.1	s__Planktophila sp009705025	85.4367	201	431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	97.98	97.98	0.75	0.75	2	-
GCA_903858325.1	s__Planktophila sp903858325	82.2206	250	431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000378885.1	s__Planktophila sp000378885	77.9337	108	431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.66	96.52	0.78	0.69	3	-
GCA_903918325.1	s__Planktophila sp903918325	77.4776	78	431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.89	98.77	0.80	0.78	4	-
GCA_903865885.1	s__Planktophila sp903865885	77.3501	68	431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009705165.1	s__Planktophila sp009705165	77.3268	60	431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969355.1	s__Planktophila sp018969355	77.2906	86	431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903852955.1	s__Planktophila sp903852955	77.2197	74	431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.15	97.52	0.82	0.77	4	-
GCF_002288065.1	s__Planktophila sulfonica	77.0126	98	431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009726135.1	s__Planktophila sp009726135	77.0046	94	431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.91	99.82	0.93	0.91	6	-
GCA_903845465.1	s__Planktophila sp903845465	76.7929	78	431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.37	98.68	0.87	0.84	5	-
--------------------------------------------------------------------------------
[2023-06-08 00:04:05,290] [INFO] GTDB search result was written to GCA_945898065.1_MsH-30apr19-344_genomic.fna/result_gtdb.tsv
[2023-06-08 00:04:05,290] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:04:05,293] [INFO] DFAST_QC result json was written to GCA_945898065.1_MsH-30apr19-344_genomic.fna/dqc_result.json
[2023-06-08 00:04:05,294] [INFO] DFAST_QC completed!
[2023-06-08 00:04:05,294] [INFO] Total running time: 0h0m32s