[2023-03-16 05:52:41,081] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:52:41,081] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:52:41,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg34768853-8c69-4dc9-813c-ffd8c11161c1/dqc_reference
[2023-03-16 05:52:42,181] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:52:42,181] [INFO] Task started: Prodigal
[2023-03-16 05:52:42,181] [INFO] Running command: cat /var/lib/cwl/stg279c2135-9bfe-476d-8881-58ee6112214f/OceanDNA-b21061.fa | prodigal -d OceanDNA-b21061/cds.fna -a OceanDNA-b21061/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:52:48,796] [INFO] Task succeeded: Prodigal
[2023-03-16 05:52:48,796] [INFO] Task started: HMMsearch
[2023-03-16 05:52:48,796] [INFO] Running command: hmmsearch --tblout OceanDNA-b21061/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34768853-8c69-4dc9-813c-ffd8c11161c1/dqc_reference/reference_markers.hmm OceanDNA-b21061/protein.faa > /dev/null
[2023-03-16 05:52:48,988] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:52:48,988] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg279c2135-9bfe-476d-8881-58ee6112214f/OceanDNA-b21061.fa]
[2023-03-16 05:52:49,005] [INFO] Query marker FASTA was written to OceanDNA-b21061/markers.fasta
[2023-03-16 05:52:49,005] [INFO] Task started: Blastn
[2023-03-16 05:52:49,006] [INFO] Running command: blastn -query OceanDNA-b21061/markers.fasta -db /var/lib/cwl/stg34768853-8c69-4dc9-813c-ffd8c11161c1/dqc_reference/reference_markers.fasta -out OceanDNA-b21061/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:52:49,560] [INFO] Task succeeded: Blastn
[2023-03-16 05:52:49,562] [INFO] Selected 18 target genomes.
[2023-03-16 05:52:49,562] [INFO] Target genome list was writen to OceanDNA-b21061/target_genomes.txt
[2023-03-16 05:52:49,605] [INFO] Task started: fastANI
[2023-03-16 05:52:49,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg279c2135-9bfe-476d-8881-58ee6112214f/OceanDNA-b21061.fa --refList OceanDNA-b21061/target_genomes.txt --output OceanDNA-b21061/fastani_result.tsv --threads 1
[2023-03-16 05:53:00,058] [INFO] Task succeeded: fastANI
[2023-03-16 05:53:00,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34768853-8c69-4dc9-813c-ffd8c11161c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:53:00,058] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34768853-8c69-4dc9-813c-ffd8c11161c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:53:00,059] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:53:00,059] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:53:00,059] [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
--------------------------------------------------------------------------------
[2023-03-16 05:53:00,059] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21061/tc_result.tsv
[2023-03-16 05:53:00,059] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:53:00,060] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:53:00,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34768853-8c69-4dc9-813c-ffd8c11161c1/dqc_reference/checkm_data
[2023-03-16 05:53:00,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:53:00,106] [INFO] Task started: CheckM
[2023-03-16 05:53:00,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21061/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21061/checkm_input OceanDNA-b21061/checkm_result
[2023-03-16 05:53:22,939] [INFO] Task succeeded: CheckM
[2023-03-16 05:53:22,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.27%
Contamintation: 5.59%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-16 05:53:22,944] [INFO] ===== Completeness check finished =====
[2023-03-16 05:53:22,944] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:53:22,944] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21061/markers.fasta)
[2023-03-16 05:53:22,945] [INFO] Task started: Blastn
[2023-03-16 05:53:22,945] [INFO] Running command: blastn -query OceanDNA-b21061/markers.fasta -db /var/lib/cwl/stg34768853-8c69-4dc9-813c-ffd8c11161c1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21061/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:53:23,675] [INFO] Task succeeded: Blastn
[2023-03-16 05:53:23,677] [INFO] Selected 14 target genomes.
[2023-03-16 05:53:23,677] [INFO] Target genome list was writen to OceanDNA-b21061/target_genomes_gtdb.txt
[2023-03-16 05:53:23,696] [INFO] Task started: fastANI
[2023-03-16 05:53:23,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg279c2135-9bfe-476d-8881-58ee6112214f/OceanDNA-b21061.fa --refList OceanDNA-b21061/target_genomes_gtdb.txt --output OceanDNA-b21061/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:53:28,857] [INFO] Task succeeded: fastANI
[2023-03-16 05:53:28,862] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:53:28,862] [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_018702695.1	s__LS-NOB sp018702695	98.984	232	268	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.34	99.32	0.82	0.80	4	conclusive
GCA_003545625.1	s__LS-NOB sp003545625	77.4852	73	268	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	98.65	98.65	0.77	0.77	2	-
GCA_018653085.1	s__LS-NOB sp018653085	77.4368	124	268	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	-
GCA_001542995.1	s__LS-NOB sp001542995	77.2721	91	268	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382285.1	s__LS-NOB sp014382285	77.2303	117	268	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.85	99.85	0.92	0.92	2	-
GCA_018664975.1	s__LS-NOB sp018664975	76.7029	78	268	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:53:28,863] [INFO] GTDB search result was written to OceanDNA-b21061/result_gtdb.tsv
[2023-03-16 05:53:28,863] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:53:28,865] [INFO] DFAST_QC result json was written to OceanDNA-b21061/dqc_result.json
[2023-03-16 05:53:28,865] [INFO] DFAST_QC completed!
[2023-03-16 05:53:28,865] [INFO] Total running time: 0h0m48s