[2023-03-15 10:52:57,311] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,318] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,318] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f4960f4-1f27-4a25-8005-d77a0ecabd5e/dqc_reference
[2023-03-15 10:52:58,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,864] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,864] [INFO] Running command: cat /var/lib/cwl/stg888a5f51-617f-4eca-9baa-50b55d2706c2/OceanDNA-b15551.fa | prodigal -d OceanDNA-b15551/cds.fna -a OceanDNA-b15551/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:18,225] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:18,225] [INFO] Task started: HMMsearch
[2023-03-15 10:53:18,225] [INFO] Running command: hmmsearch --tblout OceanDNA-b15551/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f4960f4-1f27-4a25-8005-d77a0ecabd5e/dqc_reference/reference_markers.hmm OceanDNA-b15551/protein.faa > /dev/null
[2023-03-15 10:53:18,428] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:18,429] [INFO] Found 6/6 markers.
[2023-03-15 10:53:18,452] [INFO] Query marker FASTA was written to OceanDNA-b15551/markers.fasta
[2023-03-15 10:53:18,454] [INFO] Task started: Blastn
[2023-03-15 10:53:18,454] [INFO] Running command: blastn -query OceanDNA-b15551/markers.fasta -db /var/lib/cwl/stg0f4960f4-1f27-4a25-8005-d77a0ecabd5e/dqc_reference/reference_markers.fasta -out OceanDNA-b15551/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:18,967] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:18,968] [INFO] Selected 10 target genomes.
[2023-03-15 10:53:18,968] [INFO] Target genome list was writen to OceanDNA-b15551/target_genomes.txt
[2023-03-15 10:53:18,976] [INFO] Task started: fastANI
[2023-03-15 10:53:18,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg888a5f51-617f-4eca-9baa-50b55d2706c2/OceanDNA-b15551.fa --refList OceanDNA-b15551/target_genomes.txt --output OceanDNA-b15551/fastani_result.tsv --threads 1
[2023-03-15 10:53:24,202] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:24,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f4960f4-1f27-4a25-8005-d77a0ecabd5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:24,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f4960f4-1f27-4a25-8005-d77a0ecabd5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:24,203] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:24,203] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:53:24,203] [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
--------------------------------------------------------------------------------
[2023-03-15 10:53:24,203] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15551/tc_result.tsv
[2023-03-15 10:53:24,203] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:24,203] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:24,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f4960f4-1f27-4a25-8005-d77a0ecabd5e/dqc_reference/checkm_data
[2023-03-15 10:53:24,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:24,337] [INFO] Task started: CheckM
[2023-03-15 10:53:24,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15551/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15551/checkm_input OceanDNA-b15551/checkm_result
[2023-03-15 10:54:16,388] [INFO] Task succeeded: CheckM
[2023-03-15 10:54:16,389] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 10:54:16,391] [INFO] ===== Completeness check finished =====
[2023-03-15 10:54:16,392] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:54:16,392] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15551/markers.fasta)
[2023-03-15 10:54:16,393] [INFO] Task started: Blastn
[2023-03-15 10:54:16,393] [INFO] Running command: blastn -query OceanDNA-b15551/markers.fasta -db /var/lib/cwl/stg0f4960f4-1f27-4a25-8005-d77a0ecabd5e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15551/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:54:17,102] [INFO] Task succeeded: Blastn
[2023-03-15 10:54:17,103] [INFO] Selected 22 target genomes.
[2023-03-15 10:54:17,103] [INFO] Target genome list was writen to OceanDNA-b15551/target_genomes_gtdb.txt
[2023-03-15 10:54:17,128] [INFO] Task started: fastANI
[2023-03-15 10:54:17,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg888a5f51-617f-4eca-9baa-50b55d2706c2/OceanDNA-b15551.fa --refList OceanDNA-b15551/target_genomes_gtdb.txt --output OceanDNA-b15551/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:54:29,357] [INFO] Task succeeded: fastANI
[2023-03-15 10:54:29,362] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:54:29,362] [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_002401285.1	s__UBA11650 sp002401285	98.8683	747	1014	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	98.75	98.75	0.80	0.80	2	conclusive
GCA_002710215.1	s__UBA11650 sp002710215	91.2487	708	1014	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	99.22	99.06	0.76	0.73	3	-
GCA_002708395.1	s__UBA11650 sp002708395	80.4919	424	1014	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	98.39	98.39	0.67	0.67	2	-
GCA_002721995.1	s__UBA9611 sp002721995	76.3226	106	1014	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	76.1297	83	1014	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840175.1	s__VXOI01 sp009840175	76.0143	85	1014	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__VXOI01	95.0	99.70	99.70	0.91	0.91	2	-
GCA_002238825.1	s__Bin87 sp002238825	75.9482	79	1014	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin87	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:54:29,363] [INFO] GTDB search result was written to OceanDNA-b15551/result_gtdb.tsv
[2023-03-15 10:54:29,363] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:54:29,363] [INFO] DFAST_QC result json was written to OceanDNA-b15551/dqc_result.json
[2023-03-15 10:54:29,364] [INFO] DFAST_QC completed!
[2023-03-15 10:54:29,364] [INFO] Total running time: 0h1m32s