[2023-03-16 13:29:13,376] [INFO] DFAST_QC pipeline started.
[2023-03-16 13:29:13,377] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 13:29:13,377] [INFO] DQC Reference Directory: /var/lib/cwl/stg06fcbbde-46c4-400f-a374-01d97f297501/dqc_reference
[2023-03-16 13:29:20,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 13:29:20,400] [INFO] Task started: Prodigal
[2023-03-16 13:29:20,400] [INFO] Running command: cat /var/lib/cwl/stg7aff472f-2c1b-40b0-bd10-149346047e26/OceanDNA-b34784.fa | prodigal -d OceanDNA-b34784/cds.fna -a OceanDNA-b34784/protein.faa -g 11 -q > /dev/null
[2023-03-16 13:29:38,117] [INFO] Task succeeded: Prodigal
[2023-03-16 13:29:38,117] [INFO] Task started: HMMsearch
[2023-03-16 13:29:38,117] [INFO] Running command: hmmsearch --tblout OceanDNA-b34784/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06fcbbde-46c4-400f-a374-01d97f297501/dqc_reference/reference_markers.hmm OceanDNA-b34784/protein.faa > /dev/null
[2023-03-16 13:29:38,382] [INFO] Task succeeded: HMMsearch
[2023-03-16 13:29:38,383] [INFO] Found 6/6 markers.
[2023-03-16 13:29:38,399] [INFO] Query marker FASTA was written to OceanDNA-b34784/markers.fasta
[2023-03-16 13:29:38,400] [INFO] Task started: Blastn
[2023-03-16 13:29:38,400] [INFO] Running command: blastn -query OceanDNA-b34784/markers.fasta -db /var/lib/cwl/stg06fcbbde-46c4-400f-a374-01d97f297501/dqc_reference/reference_markers.fasta -out OceanDNA-b34784/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:29:42,884] [INFO] Task succeeded: Blastn
[2023-03-16 13:29:42,885] [INFO] Selected 28 target genomes.
[2023-03-16 13:29:42,885] [INFO] Target genome list was writen to OceanDNA-b34784/target_genomes.txt
[2023-03-16 13:29:42,902] [INFO] Task started: fastANI
[2023-03-16 13:29:42,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg7aff472f-2c1b-40b0-bd10-149346047e26/OceanDNA-b34784.fa --refList OceanDNA-b34784/target_genomes.txt --output OceanDNA-b34784/fastani_result.tsv --threads 1
[2023-03-16 13:30:12,143] [INFO] Task succeeded: fastANI
[2023-03-16 13:30:12,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06fcbbde-46c4-400f-a374-01d97f297501/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 13:30:12,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06fcbbde-46c4-400f-a374-01d97f297501/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 13:30:12,315] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 13:30:12,315] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 13:30:12,315] [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
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	76.9262	52	711	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 13:30:12,315] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34784/tc_result.tsv
[2023-03-16 13:30:12,316] [INFO] ===== Taxonomy check completed =====
[2023-03-16 13:30:12,316] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 13:30:12,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06fcbbde-46c4-400f-a374-01d97f297501/dqc_reference/checkm_data
[2023-03-16 13:30:12,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 13:30:12,339] [INFO] Task started: CheckM
[2023-03-16 13:30:12,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34784/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34784/checkm_input OceanDNA-b34784/checkm_result
[2023-03-16 13:30:56,076] [INFO] Task succeeded: CheckM
[2023-03-16 13:30:56,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.95%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 13:30:56,078] [INFO] ===== Completeness check finished =====
[2023-03-16 13:30:56,079] [INFO] ===== Start GTDB Search =====
[2023-03-16 13:30:56,079] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34784/markers.fasta)
[2023-03-16 13:30:56,080] [INFO] Task started: Blastn
[2023-03-16 13:30:56,080] [INFO] Running command: blastn -query OceanDNA-b34784/markers.fasta -db /var/lib/cwl/stg06fcbbde-46c4-400f-a374-01d97f297501/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34784/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:30:58,095] [INFO] Task succeeded: Blastn
[2023-03-16 13:30:58,096] [INFO] Selected 32 target genomes.
[2023-03-16 13:30:58,096] [INFO] Target genome list was writen to OceanDNA-b34784/target_genomes_gtdb.txt
[2023-03-16 13:30:58,664] [INFO] Task started: fastANI
[2023-03-16 13:30:58,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg7aff472f-2c1b-40b0-bd10-149346047e26/OceanDNA-b34784.fa --refList OceanDNA-b34784/target_genomes_gtdb.txt --output OceanDNA-b34784/fastani_result_gtdb.tsv --threads 1
[2023-03-16 13:31:22,124] [INFO] Task succeeded: fastANI
[2023-03-16 13:31:22,129] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 13:31:22,129] [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
GCF_000155775.1	s__Glaciecola sp000155775	77.3659	104	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292215.1	s__Glaciecola sp002292215	77.2926	103	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	99.49	98.83	0.91	0.88	4	-
GCA_014872805.1	s__Glaciecola sp014872805	77.1678	125	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003203515.1	s__Glaciecola sp003203515	77.127	56	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623155.1	s__Glaciecola sp018623155	77.0113	104	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506055.1	s__Alteromonas lipotrueae	76.9748	51	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCF_006538345.1	s__Alteromonas sp006538345	76.7685	50	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 13:31:22,130] [INFO] GTDB search result was written to OceanDNA-b34784/result_gtdb.tsv
[2023-03-16 13:31:22,130] [INFO] ===== GTDB Search completed =====
[2023-03-16 13:31:22,130] [INFO] DFAST_QC result json was written to OceanDNA-b34784/dqc_result.json
[2023-03-16 13:31:22,131] [INFO] DFAST_QC completed!
[2023-03-16 13:31:22,131] [INFO] Total running time: 0h2m9s