[2023-03-19 02:59:38,477] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:59:38,477] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:59:38,477] [INFO] DQC Reference Directory: /var/lib/cwl/stgde8257b0-6ab6-4812-b185-384e725a4041/dqc_reference
[2023-03-19 02:59:39,546] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:59:39,546] [INFO] Task started: Prodigal
[2023-03-19 02:59:39,547] [INFO] Running command: cat /var/lib/cwl/stg16c514dc-dfc8-421d-b238-e4e1462ad58b/OceanDNA-b15052.fa | prodigal -d OceanDNA-b15052/cds.fna -a OceanDNA-b15052/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:59:45,844] [INFO] Task succeeded: Prodigal
[2023-03-19 02:59:45,844] [INFO] Task started: HMMsearch
[2023-03-19 02:59:45,844] [INFO] Running command: hmmsearch --tblout OceanDNA-b15052/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde8257b0-6ab6-4812-b185-384e725a4041/dqc_reference/reference_markers.hmm OceanDNA-b15052/protein.faa > /dev/null
[2023-03-19 02:59:45,992] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:59:45,992] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg16c514dc-dfc8-421d-b238-e4e1462ad58b/OceanDNA-b15052.fa]
[2023-03-19 02:59:46,003] [INFO] Query marker FASTA was written to OceanDNA-b15052/markers.fasta
[2023-03-19 02:59:46,004] [INFO] Task started: Blastn
[2023-03-19 02:59:46,004] [INFO] Running command: blastn -query OceanDNA-b15052/markers.fasta -db /var/lib/cwl/stgde8257b0-6ab6-4812-b185-384e725a4041/dqc_reference/reference_markers.fasta -out OceanDNA-b15052/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:59:46,501] [INFO] Task succeeded: Blastn
[2023-03-19 02:59:46,502] [INFO] Selected 12 target genomes.
[2023-03-19 02:59:46,502] [INFO] Target genome list was writen to OceanDNA-b15052/target_genomes.txt
[2023-03-19 02:59:46,509] [INFO] Task started: fastANI
[2023-03-19 02:59:46,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg16c514dc-dfc8-421d-b238-e4e1462ad58b/OceanDNA-b15052.fa --refList OceanDNA-b15052/target_genomes.txt --output OceanDNA-b15052/fastani_result.tsv --threads 1
[2023-03-19 02:59:51,985] [INFO] Task succeeded: fastANI
[2023-03-19 02:59:51,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde8257b0-6ab6-4812-b185-384e725a4041/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:59:51,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde8257b0-6ab6-4812-b185-384e725a4041/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:59:51,985] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:59:51,985] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:59:51,985] [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
--------------------------------------------------------------------------------
[2023-03-19 02:59:51,987] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15052/tc_result.tsv
[2023-03-19 02:59:51,989] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:59:51,990] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:59:51,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde8257b0-6ab6-4812-b185-384e725a4041/dqc_reference/checkm_data
[2023-03-19 02:59:51,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:59:51,996] [INFO] Task started: CheckM
[2023-03-19 02:59:51,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15052/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15052/checkm_input OceanDNA-b15052/checkm_result
[2023-03-19 03:00:13,250] [INFO] Task succeeded: CheckM
[2023-03-19 03:00:13,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:00:13,253] [INFO] ===== Completeness check finished =====
[2023-03-19 03:00:13,253] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:00:13,254] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15052/markers.fasta)
[2023-03-19 03:00:13,255] [INFO] Task started: Blastn
[2023-03-19 03:00:13,255] [INFO] Running command: blastn -query OceanDNA-b15052/markers.fasta -db /var/lib/cwl/stgde8257b0-6ab6-4812-b185-384e725a4041/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15052/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:00:13,953] [INFO] Task succeeded: Blastn
[2023-03-19 03:00:13,954] [INFO] Selected 9 target genomes.
[2023-03-19 03:00:13,954] [INFO] Target genome list was writen to OceanDNA-b15052/target_genomes_gtdb.txt
[2023-03-19 03:00:13,963] [INFO] Task started: fastANI
[2023-03-19 03:00:13,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg16c514dc-dfc8-421d-b238-e4e1462ad58b/OceanDNA-b15052.fa --refList OceanDNA-b15052/target_genomes_gtdb.txt --output OceanDNA-b15052/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:00:16,241] [INFO] Task succeeded: fastANI
[2023-03-19 03:00:16,246] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:00:16,247] [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_002719425.1	s__TMED-70 sp002719425	99.3463	331	421	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002703265.1	s__TMED-70 sp002703265	88.2638	372	421	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	97.70	96.59	0.89	0.70	8	-
GCA_002711965.1	s__TMED-70 sp002711965	78.8873	209	421	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	98.97	98.97	0.82	0.82	2	-
GCA_002699165.1	s__TMED-70 sp002699165	78.6772	234	421	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	99.00	98.33	0.87	0.75	4	-
GCA_002710135.1	s__TMED-70 sp002710135	78.519	152	421	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721875.1	s__TMED-70 sp002721875	77.5413	139	421	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937255.1	s__TMED-70 sp009937255	77.4547	146	421	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	96.35	96.35	0.92	0.92	2	-
GCA_002718455.1	s__GCA-2718455 sp002718455	76.7962	98	421	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-2718455	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:00:16,248] [INFO] GTDB search result was written to OceanDNA-b15052/result_gtdb.tsv
[2023-03-19 03:00:16,248] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:00:16,249] [INFO] DFAST_QC result json was written to OceanDNA-b15052/dqc_result.json
[2023-03-19 03:00:16,249] [INFO] DFAST_QC completed!
[2023-03-19 03:00:16,249] [INFO] Total running time: 0h0m38s