[2023-03-17 11:57:21,088] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:21,088] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:21,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg3796174d-ed7e-48d8-900d-611f0510f352/dqc_reference
[2023-03-17 11:57:22,180] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:22,180] [INFO] Task started: Prodigal
[2023-03-17 11:57:22,180] [INFO] Running command: cat /var/lib/cwl/stged7e4e1f-c395-4961-929e-733a98e40040/OceanDNA-b44876.fa | prodigal -d OceanDNA-b44876/cds.fna -a OceanDNA-b44876/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:43,609] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:43,609] [INFO] Task started: HMMsearch
[2023-03-17 11:57:43,609] [INFO] Running command: hmmsearch --tblout OceanDNA-b44876/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3796174d-ed7e-48d8-900d-611f0510f352/dqc_reference/reference_markers.hmm OceanDNA-b44876/protein.faa > /dev/null
[2023-03-17 11:57:43,811] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:43,811] [INFO] Found 6/6 markers.
[2023-03-17 11:57:43,829] [INFO] Query marker FASTA was written to OceanDNA-b44876/markers.fasta
[2023-03-17 11:57:43,829] [INFO] Task started: Blastn
[2023-03-17 11:57:43,829] [INFO] Running command: blastn -query OceanDNA-b44876/markers.fasta -db /var/lib/cwl/stg3796174d-ed7e-48d8-900d-611f0510f352/dqc_reference/reference_markers.fasta -out OceanDNA-b44876/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:44,382] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:44,383] [INFO] Selected 15 target genomes.
[2023-03-17 11:57:44,383] [INFO] Target genome list was writen to OceanDNA-b44876/target_genomes.txt
[2023-03-17 11:57:44,392] [INFO] Task started: fastANI
[2023-03-17 11:57:44,392] [INFO] Running command: fastANI --query /var/lib/cwl/stged7e4e1f-c395-4961-929e-733a98e40040/OceanDNA-b44876.fa --refList OceanDNA-b44876/target_genomes.txt --output OceanDNA-b44876/fastani_result.tsv --threads 1
[2023-03-17 11:57:52,118] [INFO] Task succeeded: fastANI
[2023-03-17 11:57:52,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3796174d-ed7e-48d8-900d-611f0510f352/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:57:52,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3796174d-ed7e-48d8-900d-611f0510f352/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:57:52,118] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:57:52,119] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:57:52,119] [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
--------------------------------------------------------------------------------
[2023-03-17 11:57:52,119] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44876/tc_result.tsv
[2023-03-17 11:57:52,119] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:57:52,119] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:57:52,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3796174d-ed7e-48d8-900d-611f0510f352/dqc_reference/checkm_data
[2023-03-17 11:57:52,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:57:52,126] [INFO] Task started: CheckM
[2023-03-17 11:57:52,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44876/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44876/checkm_input OceanDNA-b44876/checkm_result
[2023-03-17 11:58:40,354] [INFO] Task succeeded: CheckM
[2023-03-17 11:58:40,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:58:40,356] [INFO] ===== Completeness check finished =====
[2023-03-17 11:58:40,357] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:58:40,357] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44876/markers.fasta)
[2023-03-17 11:58:40,357] [INFO] Task started: Blastn
[2023-03-17 11:58:40,357] [INFO] Running command: blastn -query OceanDNA-b44876/markers.fasta -db /var/lib/cwl/stg3796174d-ed7e-48d8-900d-611f0510f352/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44876/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:58:41,259] [INFO] Task succeeded: Blastn
[2023-03-17 11:58:41,259] [INFO] Selected 18 target genomes.
[2023-03-17 11:58:41,260] [INFO] Target genome list was writen to OceanDNA-b44876/target_genomes_gtdb.txt
[2023-03-17 11:58:41,337] [INFO] Task started: fastANI
[2023-03-17 11:58:41,337] [INFO] Running command: fastANI --query /var/lib/cwl/stged7e4e1f-c395-4961-929e-733a98e40040/OceanDNA-b44876.fa --refList OceanDNA-b44876/target_genomes_gtdb.txt --output OceanDNA-b44876/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:58:50,074] [INFO] Task succeeded: fastANI
[2023-03-17 11:58:50,081] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:58:50,081] [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_001627865.1	s__Arctic96AD-7 sp001627865	99.876	888	929	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.71	99.45	0.95	0.94	9	conclusive
GCA_902562015.1	s__Arctic96AD-7 sp902562015	77.8086	161	929	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_002082305.1	s__Arctic96AD-7 sp002082305	77.2769	251	929	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_016764995.1	s__Arctic96AD-7 sp016764995	76.9825	207	929	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_905182865.1	s__Arctic96AD-7 sp905182865	76.886	225	929	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_002716165.1	s__Arctic96AD-7 sp002716165	76.7756	126	929	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_012964265.1	s__Arctic96AD-7 sp012964265	76.705	169	929	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_002685535.1	s__Arctic96AD-7 sp002685535	76.4154	185	929	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_018645085.1	s__Arctic96AD-7 sp018645085	76.3708	174	929	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_014382365.1	s__Arctic96AD-7 sp014382365	76.2243	168	929	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	-
GCA_004213175.1	s__Arctic96AD-7 sp002704555	76.1381	108	929	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.39	96.63	0.73	0.69	4	-
--------------------------------------------------------------------------------
[2023-03-17 11:58:50,081] [INFO] GTDB search result was written to OceanDNA-b44876/result_gtdb.tsv
[2023-03-17 11:58:50,081] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:58:50,082] [INFO] DFAST_QC result json was written to OceanDNA-b44876/dqc_result.json
[2023-03-17 11:58:50,082] [INFO] DFAST_QC completed!
[2023-03-17 11:58:50,082] [INFO] Total running time: 0h1m29s