[2023-03-19 01:25:20,234] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:25:20,234] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:25:20,234] [INFO] DQC Reference Directory: /var/lib/cwl/stga796bfcb-aee3-42d9-b9aa-049189bee559/dqc_reference
[2023-03-19 01:25:21,353] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:25:21,353] [INFO] Task started: Prodigal
[2023-03-19 01:25:21,353] [INFO] Running command: cat /var/lib/cwl/stg148f2bd4-c0e9-4b4d-8664-839ecf2a15ca/OceanDNA-b10957.fa | prodigal -d OceanDNA-b10957/cds.fna -a OceanDNA-b10957/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:25:33,251] [INFO] Task succeeded: Prodigal
[2023-03-19 01:25:33,252] [INFO] Task started: HMMsearch
[2023-03-19 01:25:33,252] [INFO] Running command: hmmsearch --tblout OceanDNA-b10957/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga796bfcb-aee3-42d9-b9aa-049189bee559/dqc_reference/reference_markers.hmm OceanDNA-b10957/protein.faa > /dev/null
[2023-03-19 01:25:33,456] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:25:33,457] [INFO] Found 6/6 markers.
[2023-03-19 01:25:33,471] [INFO] Query marker FASTA was written to OceanDNA-b10957/markers.fasta
[2023-03-19 01:25:33,472] [INFO] Task started: Blastn
[2023-03-19 01:25:33,472] [INFO] Running command: blastn -query OceanDNA-b10957/markers.fasta -db /var/lib/cwl/stga796bfcb-aee3-42d9-b9aa-049189bee559/dqc_reference/reference_markers.fasta -out OceanDNA-b10957/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:25:34,014] [INFO] Task succeeded: Blastn
[2023-03-19 01:25:34,015] [INFO] Selected 29 target genomes.
[2023-03-19 01:25:34,016] [INFO] Target genome list was writen to OceanDNA-b10957/target_genomes.txt
[2023-03-19 01:25:34,039] [INFO] Task started: fastANI
[2023-03-19 01:25:34,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg148f2bd4-c0e9-4b4d-8664-839ecf2a15ca/OceanDNA-b10957.fa --refList OceanDNA-b10957/target_genomes.txt --output OceanDNA-b10957/fastani_result.tsv --threads 1
[2023-03-19 01:25:48,717] [INFO] Task succeeded: fastANI
[2023-03-19 01:25:48,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga796bfcb-aee3-42d9-b9aa-049189bee559/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:25:48,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga796bfcb-aee3-42d9-b9aa-049189bee559/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:25:48,717] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:25:48,717] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:25:48,717] [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 01:25:48,718] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10957/tc_result.tsv
[2023-03-19 01:25:48,719] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:25:48,719] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:25:48,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga796bfcb-aee3-42d9-b9aa-049189bee559/dqc_reference/checkm_data
[2023-03-19 01:25:48,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:25:48,726] [INFO] Task started: CheckM
[2023-03-19 01:25:48,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10957/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10957/checkm_input OceanDNA-b10957/checkm_result
[2023-03-19 01:26:22,300] [INFO] Task succeeded: CheckM
[2023-03-19 01:26:22,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:26:22,302] [INFO] ===== Completeness check finished =====
[2023-03-19 01:26:22,302] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:26:22,302] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10957/markers.fasta)
[2023-03-19 01:26:22,303] [INFO] Task started: Blastn
[2023-03-19 01:26:22,303] [INFO] Running command: blastn -query OceanDNA-b10957/markers.fasta -db /var/lib/cwl/stga796bfcb-aee3-42d9-b9aa-049189bee559/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10957/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:26:23,056] [INFO] Task succeeded: Blastn
[2023-03-19 01:26:23,057] [INFO] Selected 26 target genomes.
[2023-03-19 01:26:23,057] [INFO] Target genome list was writen to OceanDNA-b10957/target_genomes_gtdb.txt
[2023-03-19 01:26:23,088] [INFO] Task started: fastANI
[2023-03-19 01:26:23,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg148f2bd4-c0e9-4b4d-8664-839ecf2a15ca/OceanDNA-b10957.fa --refList OceanDNA-b10957/target_genomes_gtdb.txt --output OceanDNA-b10957/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:26:33,995] [INFO] Task succeeded: fastANI
[2023-03-19 01:26:33,999] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:26:34,000] [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_011526285.1	s__UBA7428 sp011526285	95.7538	474	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011526275.1	s__UBA7428 sp011526275	79.6104	267	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526335.1	s__UBA7428 sp011526335	77.0811	84	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478905.1	s__UBA7428 sp905478905	77.0203	130	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.97	98.97	0.80	0.80	2	-
GCA_011526265.1	s__UBA7428 sp011526265	76.828	86	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477625.1	s__UBA7428 sp002477625	76.0303	52	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.28	97.25	0.74	0.68	4	-
--------------------------------------------------------------------------------
[2023-03-19 01:26:34,000] [INFO] GTDB search result was written to OceanDNA-b10957/result_gtdb.tsv
[2023-03-19 01:26:34,001] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:26:34,002] [INFO] DFAST_QC result json was written to OceanDNA-b10957/dqc_result.json
[2023-03-19 01:26:34,002] [INFO] DFAST_QC completed!
[2023-03-19 01:26:34,003] [INFO] Total running time: 0h1m14s