[2023-03-19 04:29:39,708] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:39,708] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:39,708] [INFO] DQC Reference Directory: /var/lib/cwl/stg105cbb36-7d0b-448c-9c47-d21225153759/dqc_reference
[2023-03-19 04:29:40,812] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:40,812] [INFO] Task started: Prodigal
[2023-03-19 04:29:40,813] [INFO] Running command: cat /var/lib/cwl/stg22079c41-09e5-4531-83a2-53978a6ede44/OceanDNA-b8408.fa | prodigal -d OceanDNA-b8408/cds.fna -a OceanDNA-b8408/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:46,538] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:46,538] [INFO] Task started: HMMsearch
[2023-03-19 04:29:46,538] [INFO] Running command: hmmsearch --tblout OceanDNA-b8408/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg105cbb36-7d0b-448c-9c47-d21225153759/dqc_reference/reference_markers.hmm OceanDNA-b8408/protein.faa > /dev/null
[2023-03-19 04:29:46,688] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:46,689] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg22079c41-09e5-4531-83a2-53978a6ede44/OceanDNA-b8408.fa]
[2023-03-19 04:29:46,697] [INFO] Query marker FASTA was written to OceanDNA-b8408/markers.fasta
[2023-03-19 04:29:46,697] [INFO] Task started: Blastn
[2023-03-19 04:29:46,697] [INFO] Running command: blastn -query OceanDNA-b8408/markers.fasta -db /var/lib/cwl/stg105cbb36-7d0b-448c-9c47-d21225153759/dqc_reference/reference_markers.fasta -out OceanDNA-b8408/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:47,241] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:47,242] [INFO] Selected 24 target genomes.
[2023-03-19 04:29:47,242] [INFO] Target genome list was writen to OceanDNA-b8408/target_genomes.txt
[2023-03-19 04:29:47,252] [INFO] Task started: fastANI
[2023-03-19 04:29:47,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg22079c41-09e5-4531-83a2-53978a6ede44/OceanDNA-b8408.fa --refList OceanDNA-b8408/target_genomes.txt --output OceanDNA-b8408/fastani_result.tsv --threads 1
[2023-03-19 04:29:59,586] [INFO] Task succeeded: fastANI
[2023-03-19 04:29:59,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg105cbb36-7d0b-448c-9c47-d21225153759/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:29:59,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg105cbb36-7d0b-448c-9c47-d21225153759/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:29:59,587] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:29:59,587] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:29:59,587] [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 04:29:59,587] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8408/tc_result.tsv
[2023-03-19 04:29:59,587] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:29:59,587] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:29:59,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg105cbb36-7d0b-448c-9c47-d21225153759/dqc_reference/checkm_data
[2023-03-19 04:29:59,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:29:59,592] [INFO] Task started: CheckM
[2023-03-19 04:29:59,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8408/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8408/checkm_input OceanDNA-b8408/checkm_result
[2023-03-19 04:30:19,724] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:19,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.18%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:19,726] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:19,726] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:19,726] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8408/markers.fasta)
[2023-03-19 04:30:19,726] [INFO] Task started: Blastn
[2023-03-19 04:30:19,726] [INFO] Running command: blastn -query OceanDNA-b8408/markers.fasta -db /var/lib/cwl/stg105cbb36-7d0b-448c-9c47-d21225153759/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8408/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:20,528] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:20,529] [INFO] Selected 8 target genomes.
[2023-03-19 04:30:20,529] [INFO] Target genome list was writen to OceanDNA-b8408/target_genomes_gtdb.txt
[2023-03-19 04:30:20,556] [INFO] Task started: fastANI
[2023-03-19 04:30:20,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg22079c41-09e5-4531-83a2-53978a6ede44/OceanDNA-b8408.fa --refList OceanDNA-b8408/target_genomes_gtdb.txt --output OceanDNA-b8408/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:22,309] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:22,315] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:30:22,315] [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_004214015.1	s__MED-G11 sp004214015	97.7917	200	318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.90	97.77	0.83	0.80	4	conclusive
GCA_016777325.1	s__MED-G11 sp016777325	91.6605	190	318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509805.1	s__MED-G11 sp902509805	90.2263	149	318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.79	97.79	0.58	0.58	2	-
GCA_018646865.1	s__MED-G11 sp014239615	85.6639	271	318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.76	99.49	0.92	0.80	17	-
GCA_902514615.1	s__MED-G11 sp902514615	84.3196	212	318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239665.1	s__MED-G11 sp014239665	83.0401	246	318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.49	96.27	0.81	0.77	10	-
GCA_002457075.1	s__MED-G11 sp002457075	82.6348	194	318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	98.35	98.35	0.79	0.79	2	-
GCA_016780245.1	s__MED-G11 sp016780245	78.4899	149	318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.94	99.94	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:22,315] [INFO] GTDB search result was written to OceanDNA-b8408/result_gtdb.tsv
[2023-03-19 04:30:22,315] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:22,316] [INFO] DFAST_QC result json was written to OceanDNA-b8408/dqc_result.json
[2023-03-19 04:30:22,316] [INFO] DFAST_QC completed!
[2023-03-19 04:30:22,316] [INFO] Total running time: 0h0m43s