[2023-03-18 03:09:33,542] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:33,542] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:33,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fd05e10-32b6-4c76-a833-fa1b06ff6134/dqc_reference
[2023-03-18 03:09:34,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:34,689] [INFO] Task started: Prodigal
[2023-03-18 03:09:34,689] [INFO] Running command: cat /var/lib/cwl/stg6700420b-322e-4fba-b912-632c60189a54/OceanDNA-b36415.fa | prodigal -d OceanDNA-b36415/cds.fna -a OceanDNA-b36415/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:43,489] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:43,489] [INFO] Task started: HMMsearch
[2023-03-18 03:09:43,489] [INFO] Running command: hmmsearch --tblout OceanDNA-b36415/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fd05e10-32b6-4c76-a833-fa1b06ff6134/dqc_reference/reference_markers.hmm OceanDNA-b36415/protein.faa > /dev/null
[2023-03-18 03:09:43,714] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:43,715] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6700420b-322e-4fba-b912-632c60189a54/OceanDNA-b36415.fa]
[2023-03-18 03:09:43,733] [INFO] Query marker FASTA was written to OceanDNA-b36415/markers.fasta
[2023-03-18 03:09:43,733] [INFO] Task started: Blastn
[2023-03-18 03:09:43,733] [INFO] Running command: blastn -query OceanDNA-b36415/markers.fasta -db /var/lib/cwl/stg1fd05e10-32b6-4c76-a833-fa1b06ff6134/dqc_reference/reference_markers.fasta -out OceanDNA-b36415/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:44,239] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:44,240] [INFO] Selected 18 target genomes.
[2023-03-18 03:09:44,240] [INFO] Target genome list was writen to OceanDNA-b36415/target_genomes.txt
[2023-03-18 03:09:44,251] [INFO] Task started: fastANI
[2023-03-18 03:09:44,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg6700420b-322e-4fba-b912-632c60189a54/OceanDNA-b36415.fa --refList OceanDNA-b36415/target_genomes.txt --output OceanDNA-b36415/fastani_result.tsv --threads 1
[2023-03-18 03:09:56,566] [INFO] Task succeeded: fastANI
[2023-03-18 03:09:56,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fd05e10-32b6-4c76-a833-fa1b06ff6134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:09:56,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fd05e10-32b6-4c76-a833-fa1b06ff6134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:09:56,573] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:09:56,573] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:09:56,573] [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
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	88.6496	297	327	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	80.7887	193	327	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	80.6095	210	327	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	80.5784	194	327	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	80.0676	191	327	95	below_threshold
Alcanivorax dieselolei	strain=CGMCC 1.3690	GCA_014644575.1	285091	285091	type	True	78.0304	90	327	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	78.0255	115	327	95	below_threshold
Alcanivorax dieselolei	strain=B5	GCA_000300005.1	285091	285091	type	True	78.0111	89	327	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	77.8601	89	327	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:09:56,573] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36415/tc_result.tsv
[2023-03-18 03:09:56,573] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:09:56,574] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:09:56,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fd05e10-32b6-4c76-a833-fa1b06ff6134/dqc_reference/checkm_data
[2023-03-18 03:09:56,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:09:56,587] [INFO] Task started: CheckM
[2023-03-18 03:09:56,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36415/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36415/checkm_input OceanDNA-b36415/checkm_result
[2023-03-18 03:10:24,188] [INFO] Task succeeded: CheckM
[2023-03-18 03:10:24,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:10:24,191] [INFO] ===== Completeness check finished =====
[2023-03-18 03:10:24,191] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:10:24,191] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36415/markers.fasta)
[2023-03-18 03:10:24,191] [INFO] Task started: Blastn
[2023-03-18 03:10:24,191] [INFO] Running command: blastn -query OceanDNA-b36415/markers.fasta -db /var/lib/cwl/stg1fd05e10-32b6-4c76-a833-fa1b06ff6134/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36415/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:24,708] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:24,709] [INFO] Selected 12 target genomes.
[2023-03-18 03:10:24,709] [INFO] Target genome list was writen to OceanDNA-b36415/target_genomes_gtdb.txt
[2023-03-18 03:10:24,786] [INFO] Task started: fastANI
[2023-03-18 03:10:24,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg6700420b-322e-4fba-b912-632c60189a54/OceanDNA-b36415.fa --refList OceanDNA-b36415/target_genomes_gtdb.txt --output OceanDNA-b36415/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:10:33,140] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:33,146] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:10:33,146] [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_014762765.1	s__Alcanivorax sp014762765	97.9704	299	327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003862375.1	s__Alcanivorax jadensis_A	90.947	309	327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.67	99.67	0.92	0.92	2	-
GCF_900107995.1	s__Alcanivorax sp900107995	89.5869	305	327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	-
GCF_000756655.1	s__Alcanivorax jadensis	88.6496	297	327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	-
GCF_000155615.1	s__Alcanivorax sp000155615	80.9533	233	327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.69	0.92	0.89	4	-
GCF_000756665.1	s__Alcanivorax nanhaiticus	80.821	192	327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794965.1	s__Alcanivorax sp017794965	80.7292	215	327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300995.1	s__Alcanivorax hongdengensis	80.6688	208	327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601165.1	s__Alcanivorax sediminis	80.6208	192	327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:10:33,146] [INFO] GTDB search result was written to OceanDNA-b36415/result_gtdb.tsv
[2023-03-18 03:10:33,147] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:10:33,148] [INFO] DFAST_QC result json was written to OceanDNA-b36415/dqc_result.json
[2023-03-18 03:10:33,148] [INFO] DFAST_QC completed!
[2023-03-18 03:10:33,148] [INFO] Total running time: 0h0m60s