[2023-06-05 00:14:21,776] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:14:21,783] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:14:21,783] [INFO] DQC Reference Directory: /var/lib/cwl/stg0017fc3c-b48e-422f-ae23-7af3b387629c/dqc_reference
[2023-06-05 00:14:23,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:14:23,027] [INFO] Task started: Prodigal
[2023-06-05 00:14:23,027] [INFO] Running command: gunzip -c /var/lib/cwl/stg113def99-46a8-4b60-95c1-28b4582562f5/GCA_902607365.1_AG-464-F20_genomic.fna.gz | prodigal -d GCA_902607365.1_AG-464-F20_genomic.fna/cds.fna -a GCA_902607365.1_AG-464-F20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:14:26,777] [INFO] Task succeeded: Prodigal
[2023-06-05 00:14:26,777] [INFO] Task started: HMMsearch
[2023-06-05 00:14:26,777] [INFO] Running command: hmmsearch --tblout GCA_902607365.1_AG-464-F20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0017fc3c-b48e-422f-ae23-7af3b387629c/dqc_reference/reference_markers.hmm GCA_902607365.1_AG-464-F20_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:14:27,065] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:14:27,066] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg113def99-46a8-4b60-95c1-28b4582562f5/GCA_902607365.1_AG-464-F20_genomic.fna.gz]
[2023-06-05 00:14:27,090] [INFO] Query marker FASTA was written to GCA_902607365.1_AG-464-F20_genomic.fna/markers.fasta
[2023-06-05 00:14:27,090] [INFO] Task started: Blastn
[2023-06-05 00:14:27,090] [INFO] Running command: blastn -query GCA_902607365.1_AG-464-F20_genomic.fna/markers.fasta -db /var/lib/cwl/stg0017fc3c-b48e-422f-ae23-7af3b387629c/dqc_reference/reference_markers.fasta -out GCA_902607365.1_AG-464-F20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:28,636] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:28,645] [INFO] Selected 5 target genomes.
[2023-06-05 00:14:28,645] [INFO] Target genome list was writen to GCA_902607365.1_AG-464-F20_genomic.fna/target_genomes.txt
[2023-06-05 00:14:28,647] [INFO] Task started: fastANI
[2023-06-05 00:14:28,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg113def99-46a8-4b60-95c1-28b4582562f5/GCA_902607365.1_AG-464-F20_genomic.fna.gz --refList GCA_902607365.1_AG-464-F20_genomic.fna/target_genomes.txt --output GCA_902607365.1_AG-464-F20_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:14:30,381] [INFO] Task succeeded: fastANI
[2023-06-05 00:14:30,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0017fc3c-b48e-422f-ae23-7af3b387629c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:14:30,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0017fc3c-b48e-422f-ae23-7af3b387629c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:14:30,384] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:14:30,384] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:14:30,384] [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
--------------------------------------------------------------------------------
[2023-06-05 00:14:30,386] [INFO] DFAST Taxonomy check result was written to GCA_902607365.1_AG-464-F20_genomic.fna/tc_result.tsv
[2023-06-05 00:14:30,386] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:14:30,387] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:14:30,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0017fc3c-b48e-422f-ae23-7af3b387629c/dqc_reference/checkm_data
[2023-06-05 00:14:30,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:14:30,410] [INFO] Task started: CheckM
[2023-06-05 00:14:30,410] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902607365.1_AG-464-F20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902607365.1_AG-464-F20_genomic.fna/checkm_input GCA_902607365.1_AG-464-F20_genomic.fna/checkm_result
[2023-06-05 00:14:49,661] [INFO] Task succeeded: CheckM
[2023-06-05 00:14:49,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:14:49,681] [INFO] ===== Completeness check finished =====
[2023-06-05 00:14:49,682] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:14:49,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902607365.1_AG-464-F20_genomic.fna/markers.fasta)
[2023-06-05 00:14:49,683] [INFO] Task started: Blastn
[2023-06-05 00:14:49,683] [INFO] Running command: blastn -query GCA_902607365.1_AG-464-F20_genomic.fna/markers.fasta -db /var/lib/cwl/stg0017fc3c-b48e-422f-ae23-7af3b387629c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902607365.1_AG-464-F20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:50,154] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:50,158] [INFO] Selected 7 target genomes.
[2023-06-05 00:14:50,159] [INFO] Target genome list was writen to GCA_902607365.1_AG-464-F20_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:14:50,162] [INFO] Task started: fastANI
[2023-06-05 00:14:50,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg113def99-46a8-4b60-95c1-28b4582562f5/GCA_902607365.1_AG-464-F20_genomic.fna.gz --refList GCA_902607365.1_AG-464-F20_genomic.fna/target_genomes_gtdb.txt --output GCA_902607365.1_AG-464-F20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:14:54,104] [INFO] Task succeeded: fastANI
[2023-06-05 00:14:54,112] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 00:14:54,112] [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_002082305.1	s__Arctic96AD-7 sp002082305	94.9387	341	510	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	98.68	95.22	0.86	0.64	13	-
GCA_905182865.1	s__Arctic96AD-7 sp905182865	91.3696	402	510	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.26	97.17	0.94	0.88	7	-
GCA_902513935.1	s__Arctic96AD-7 sp902513935	91.0004	195	510	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764995.1	s__Arctic96AD-7 sp016764995	78.8294	204	510	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685535.1	s__Arctic96AD-7 sp002685535	78.6582	181	510	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.44	95.94	0.78	0.68	5	-
GCA_012964265.1	s__Arctic96AD-7 sp012964265	78.5768	158	510	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.25	98.98	0.81	0.73	8	-
GCA_014382365.1	s__Arctic96AD-7 sp014382365	78.0391	185	510	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.95	99.95	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-05 00:14:54,114] [INFO] GTDB search result was written to GCA_902607365.1_AG-464-F20_genomic.fna/result_gtdb.tsv
[2023-06-05 00:14:54,115] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:14:54,118] [INFO] DFAST_QC result json was written to GCA_902607365.1_AG-464-F20_genomic.fna/dqc_result.json
[2023-06-05 00:14:54,118] [INFO] DFAST_QC completed!
[2023-06-05 00:14:54,118] [INFO] Total running time: 0h0m32s