[2023-06-08 03:59:55,890] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:59:55,892] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:59:55,892] [INFO] DQC Reference Directory: /var/lib/cwl/stg6248c20f-2303-4881-a0b7-6460b8ccfae0/dqc_reference
[2023-06-08 03:59:57,273] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:59:57,274] [INFO] Task started: Prodigal
[2023-06-08 03:59:57,274] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b74e9c6-863f-4cc3-893c-211f2057fe2c/GCA_902521955.1_AG-333-M17_genomic.fna.gz | prodigal -d GCA_902521955.1_AG-333-M17_genomic.fna/cds.fna -a GCA_902521955.1_AG-333-M17_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:59:58,965] [INFO] Task succeeded: Prodigal
[2023-06-08 03:59:58,965] [INFO] Task started: HMMsearch
[2023-06-08 03:59:58,965] [INFO] Running command: hmmsearch --tblout GCA_902521955.1_AG-333-M17_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6248c20f-2303-4881-a0b7-6460b8ccfae0/dqc_reference/reference_markers.hmm GCA_902521955.1_AG-333-M17_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:59:59,216] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:59:59,217] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7b74e9c6-863f-4cc3-893c-211f2057fe2c/GCA_902521955.1_AG-333-M17_genomic.fna.gz]
[2023-06-08 03:59:59,240] [INFO] Query marker FASTA was written to GCA_902521955.1_AG-333-M17_genomic.fna/markers.fasta
[2023-06-08 03:59:59,241] [INFO] Task started: Blastn
[2023-06-08 03:59:59,241] [INFO] Running command: blastn -query GCA_902521955.1_AG-333-M17_genomic.fna/markers.fasta -db /var/lib/cwl/stg6248c20f-2303-4881-a0b7-6460b8ccfae0/dqc_reference/reference_markers.fasta -out GCA_902521955.1_AG-333-M17_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:59:59,820] [INFO] Task succeeded: Blastn
[2023-06-08 03:59:59,824] [INFO] Selected 10 target genomes.
[2023-06-08 03:59:59,824] [INFO] Target genome list was writen to GCA_902521955.1_AG-333-M17_genomic.fna/target_genomes.txt
[2023-06-08 03:59:59,826] [INFO] Task started: fastANI
[2023-06-08 03:59:59,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b74e9c6-863f-4cc3-893c-211f2057fe2c/GCA_902521955.1_AG-333-M17_genomic.fna.gz --refList GCA_902521955.1_AG-333-M17_genomic.fna/target_genomes.txt --output GCA_902521955.1_AG-333-M17_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:00:04,557] [INFO] Task succeeded: fastANI
[2023-06-08 04:00:04,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6248c20f-2303-4881-a0b7-6460b8ccfae0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:00:04,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6248c20f-2303-4881-a0b7-6460b8ccfae0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:00:04,560] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:00:04,561] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 04:00:04,561] [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 04:00:04,563] [INFO] DFAST Taxonomy check result was written to GCA_902521955.1_AG-333-M17_genomic.fna/tc_result.tsv
[2023-06-08 04:00:04,564] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:00:04,564] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:00:04,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6248c20f-2303-4881-a0b7-6460b8ccfae0/dqc_reference/checkm_data
[2023-06-08 04:00:04,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:00:04,584] [INFO] Task started: CheckM
[2023-06-08 04:00:04,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902521955.1_AG-333-M17_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902521955.1_AG-333-M17_genomic.fna/checkm_input GCA_902521955.1_AG-333-M17_genomic.fna/checkm_result
[2023-06-08 04:00:18,530] [INFO] Task succeeded: CheckM
[2023-06-08 04:00:18,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 04:00:18,551] [INFO] ===== Completeness check finished =====
[2023-06-08 04:00:18,552] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:00:18,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902521955.1_AG-333-M17_genomic.fna/markers.fasta)
[2023-06-08 04:00:18,553] [INFO] Task started: Blastn
[2023-06-08 04:00:18,553] [INFO] Running command: blastn -query GCA_902521955.1_AG-333-M17_genomic.fna/markers.fasta -db /var/lib/cwl/stg6248c20f-2303-4881-a0b7-6460b8ccfae0/dqc_reference/reference_markers_gtdb.fasta -out GCA_902521955.1_AG-333-M17_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:00:19,288] [INFO] Task succeeded: Blastn
[2023-06-08 04:00:19,293] [INFO] Selected 14 target genomes.
[2023-06-08 04:00:19,293] [INFO] Target genome list was writen to GCA_902521955.1_AG-333-M17_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:00:19,311] [INFO] Task started: fastANI
[2023-06-08 04:00:19,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b74e9c6-863f-4cc3-893c-211f2057fe2c/GCA_902521955.1_AG-333-M17_genomic.fna.gz --refList GCA_902521955.1_AG-333-M17_genomic.fna/target_genomes_gtdb.txt --output GCA_902521955.1_AG-333-M17_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:00:23,220] [INFO] Task succeeded: fastANI
[2023-06-08 04:00:23,241] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 04:00:23,241] [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_902521955.1	s__Actinomarina sp902521955	100.0	297	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902519215.1	s__Actinomarina sp902519215	92.9432	228	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.27	96.27	0.84	0.84	2	-
GCA_902555055.1	s__Actinomarina sp902555055	89.3414	221	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625455.1	s__Actinomarina sp902625455	80.3509	158	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.46	97.35	0.85	0.81	4	-
GCA_902593795.1	s__Actinomarina sp902593795	79.8478	118	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.69	97.47	0.86	0.85	3	-
GCA_902555985.1	s__Actinomarina sp902555985	79.8157	114	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.40	96.59	0.85	0.83	4	-
GCA_902576605.1	s__Actinomarina sp902576605	79.6926	85	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596545.1	s__Actinomarina sp902596545	79.6527	146	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.42	98.42	0.93	0.93	2	-
GCA_902628045.1	s__Actinomarina sp902628045	78.9829	96	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213405.1	s__Actinomarina sp004213405	78.5383	75	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777845.1	s__Actinomarina sp016777845	78.5062	91	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902571385.1	s__Actinomarina sp902571385	77.6113	55	298	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.95	95.63	0.85	0.83	4	-
--------------------------------------------------------------------------------
[2023-06-08 04:00:23,244] [INFO] GTDB search result was written to GCA_902521955.1_AG-333-M17_genomic.fna/result_gtdb.tsv
[2023-06-08 04:00:23,244] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:00:23,248] [INFO] DFAST_QC result json was written to GCA_902521955.1_AG-333-M17_genomic.fna/dqc_result.json
[2023-06-08 04:00:23,248] [INFO] DFAST_QC completed!
[2023-06-08 04:00:23,249] [INFO] Total running time: 0h0m27s