[2023-03-18 21:15:24,371] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:24,371] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:24,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e20daf4-4bba-43f9-9bae-9fead1eac256/dqc_reference
[2023-03-18 21:15:25,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:25,547] [INFO] Task started: Prodigal
[2023-03-18 21:15:25,547] [INFO] Running command: cat /var/lib/cwl/stg961a74bf-81cd-435f-87fd-57c3e06c98c4/OceanDNA-b15450.fa | prodigal -d OceanDNA-b15450/cds.fna -a OceanDNA-b15450/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:41,857] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:41,857] [INFO] Task started: HMMsearch
[2023-03-18 21:15:41,857] [INFO] Running command: hmmsearch --tblout OceanDNA-b15450/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e20daf4-4bba-43f9-9bae-9fead1eac256/dqc_reference/reference_markers.hmm OceanDNA-b15450/protein.faa > /dev/null
[2023-03-18 21:15:42,038] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:42,039] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg961a74bf-81cd-435f-87fd-57c3e06c98c4/OceanDNA-b15450.fa]
[2023-03-18 21:15:42,060] [INFO] Query marker FASTA was written to OceanDNA-b15450/markers.fasta
[2023-03-18 21:15:42,061] [INFO] Task started: Blastn
[2023-03-18 21:15:42,061] [INFO] Running command: blastn -query OceanDNA-b15450/markers.fasta -db /var/lib/cwl/stg7e20daf4-4bba-43f9-9bae-9fead1eac256/dqc_reference/reference_markers.fasta -out OceanDNA-b15450/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:42,556] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:42,557] [INFO] Selected 18 target genomes.
[2023-03-18 21:15:42,557] [INFO] Target genome list was writen to OceanDNA-b15450/target_genomes.txt
[2023-03-18 21:15:42,567] [INFO] Task started: fastANI
[2023-03-18 21:15:42,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg961a74bf-81cd-435f-87fd-57c3e06c98c4/OceanDNA-b15450.fa --refList OceanDNA-b15450/target_genomes.txt --output OceanDNA-b15450/fastani_result.tsv --threads 1
[2023-03-18 21:15:54,418] [INFO] Task succeeded: fastANI
[2023-03-18 21:15:54,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e20daf4-4bba-43f9-9bae-9fead1eac256/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:15:54,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e20daf4-4bba-43f9-9bae-9fead1eac256/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:15:54,418] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:15:54,418] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:15:54,419] [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
--------------------------------------------------------------------------------
[2023-03-18 21:15:54,419] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15450/tc_result.tsv
[2023-03-18 21:15:54,419] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:15:54,419] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:15:54,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e20daf4-4bba-43f9-9bae-9fead1eac256/dqc_reference/checkm_data
[2023-03-18 21:15:54,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:15:54,483] [INFO] Task started: CheckM
[2023-03-18 21:15:54,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15450/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15450/checkm_input OceanDNA-b15450/checkm_result
[2023-03-18 21:16:36,707] [INFO] Task succeeded: CheckM
[2023-03-18 21:16:36,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:16:36,711] [INFO] ===== Completeness check finished =====
[2023-03-18 21:16:36,711] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:16:36,712] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15450/markers.fasta)
[2023-03-18 21:16:36,713] [INFO] Task started: Blastn
[2023-03-18 21:16:36,713] [INFO] Running command: blastn -query OceanDNA-b15450/markers.fasta -db /var/lib/cwl/stg7e20daf4-4bba-43f9-9bae-9fead1eac256/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15450/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:16:37,352] [INFO] Task succeeded: Blastn
[2023-03-18 21:16:37,352] [INFO] Selected 20 target genomes.
[2023-03-18 21:16:37,353] [INFO] Target genome list was writen to OceanDNA-b15450/target_genomes_gtdb.txt
[2023-03-18 21:16:37,369] [INFO] Task started: fastANI
[2023-03-18 21:16:37,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg961a74bf-81cd-435f-87fd-57c3e06c98c4/OceanDNA-b15450.fa --refList OceanDNA-b15450/target_genomes_gtdb.txt --output OceanDNA-b15450/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:16:47,633] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:47,641] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:16:47,641] [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_002746355.1	s__UBA9611 sp002746355	76.8006	163	840	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	-
GCA_002721995.1	s__UBA9611 sp002721995	76.7835	184	840	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.66	0.88	0.85	7	-
GCA_002816575.1	s__UBA9611 sp002816575	76.7799	131	840	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204585.1	s__UBA9611 sp013204585	76.5057	156	840	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698265.1	s__UBA9611 sp002698265	76.4709	109	840	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.74	98.13	0.78	0.72	6	-
GCA_009692925.1	s__SHYG01 sp009692925	76.3919	81	840	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	99.84	99.84	0.93	0.93	2	-
GCA_009392075.1	s__UBA9611 sp009392075	76.3646	96	840	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	96.71	96.71	0.58	0.58	2	-
GCA_002730485.1	s__UBA9611 sp002730485	76.2752	77	840	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392095.1	s__UBA9611 sp009391975	76.1682	123	840	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.46	97.52	0.83	0.73	9	-
GCA_002401285.1	s__UBA11650 sp002401285	76.1488	59	840	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	98.75	98.75	0.80	0.80	2	-
GCA_002710215.1	s__UBA11650 sp002710215	76.0069	65	840	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	99.22	99.06	0.76	0.73	3	-
GCA_009837355.1	s__Bin87 sp009837355	75.9092	74	840	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin87	95.0	99.97	99.97	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-18 21:16:47,642] [INFO] GTDB search result was written to OceanDNA-b15450/result_gtdb.tsv
[2023-03-18 21:16:47,642] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:16:47,643] [INFO] DFAST_QC result json was written to OceanDNA-b15450/dqc_result.json
[2023-03-18 21:16:47,643] [INFO] DFAST_QC completed!
[2023-03-18 21:16:47,643] [INFO] Total running time: 0h1m23s