[2023-03-14 10:55:58,916] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,922] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,922] [INFO] DQC Reference Directory: /var/lib/cwl/stg994a4888-1c6b-42f9-adbb-ad2a211748b8/dqc_reference
[2023-03-14 10:56:00,676] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,677] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,678] [INFO] Running command: cat /var/lib/cwl/stg9e025ee3-541a-401f-87b6-5994aef1ef23/OceanDNA-b6025.fa | prodigal -d OceanDNA-b6025/cds.fna -a OceanDNA-b6025/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:12,496] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:12,496] [INFO] Task started: HMMsearch
[2023-03-14 10:56:12,496] [INFO] Running command: hmmsearch --tblout OceanDNA-b6025/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg994a4888-1c6b-42f9-adbb-ad2a211748b8/dqc_reference/reference_markers.hmm OceanDNA-b6025/protein.faa > /dev/null
[2023-03-14 10:56:12,657] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:12,658] [INFO] Found 6/6 markers.
[2023-03-14 10:56:12,671] [INFO] Query marker FASTA was written to OceanDNA-b6025/markers.fasta
[2023-03-14 10:56:12,671] [INFO] Task started: Blastn
[2023-03-14 10:56:12,671] [INFO] Running command: blastn -query OceanDNA-b6025/markers.fasta -db /var/lib/cwl/stg994a4888-1c6b-42f9-adbb-ad2a211748b8/dqc_reference/reference_markers.fasta -out OceanDNA-b6025/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:13,217] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:13,218] [INFO] Selected 36 target genomes.
[2023-03-14 10:56:13,218] [INFO] Target genome list was writen to OceanDNA-b6025/target_genomes.txt
[2023-03-14 10:56:13,236] [INFO] Task started: fastANI
[2023-03-14 10:56:13,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e025ee3-541a-401f-87b6-5994aef1ef23/OceanDNA-b6025.fa --refList OceanDNA-b6025/target_genomes.txt --output OceanDNA-b6025/fastani_result.tsv --threads 1
[2023-03-14 10:56:33,270] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:33,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg994a4888-1c6b-42f9-adbb-ad2a211748b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:33,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg994a4888-1c6b-42f9-adbb-ad2a211748b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:33,271] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:33,271] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 10:56:33,271] [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
--------------------------------------------------------------------------------
[2023-03-14 10:56:33,312] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6025/tc_result.tsv
[2023-03-14 10:56:33,312] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:33,312] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:33,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg994a4888-1c6b-42f9-adbb-ad2a211748b8/dqc_reference/checkm_data
[2023-03-14 10:56:33,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:33,320] [INFO] Task started: CheckM
[2023-03-14 10:56:33,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6025/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6025/checkm_input OceanDNA-b6025/checkm_result
[2023-03-14 10:57:07,245] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:07,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:07,247] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:07,248] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:07,248] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6025/markers.fasta)
[2023-03-14 10:57:07,248] [INFO] Task started: Blastn
[2023-03-14 10:57:07,248] [INFO] Running command: blastn -query OceanDNA-b6025/markers.fasta -db /var/lib/cwl/stg994a4888-1c6b-42f9-adbb-ad2a211748b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6025/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:07,974] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:07,975] [INFO] Selected 17 target genomes.
[2023-03-14 10:57:07,975] [INFO] Target genome list was writen to OceanDNA-b6025/target_genomes_gtdb.txt
[2023-03-14 10:57:07,995] [INFO] Task started: fastANI
[2023-03-14 10:57:07,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e025ee3-541a-401f-87b6-5994aef1ef23/OceanDNA-b6025.fa --refList OceanDNA-b6025/target_genomes_gtdb.txt --output OceanDNA-b6025/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:15,601] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:15,608] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:57:15,608] [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_003045825.1	s__UBA10364 sp003045825	97.7143	413	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.67	96.47	0.88	0.80	20	conclusive
GCA_905478295.1	s__UBA10364 sp002387615	83.5465	384	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.55	99.11	0.94	0.89	10	-
GCA_018402665.1	s__UBA10364 sp018402665	83.1264	383	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	96.42	96.42	0.92	0.92	2	-
GCA_002685435.1	s__UBA10364 sp002685435	83.0768	304	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525035.1	s__UBA10364 sp011525035	79.6552	127	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003385605.1	s__UBA10364 sp003385605	79.5231	125	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	-
GCA_012269745.1	s__UBA10364 sp012269745	79.148	122	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911625.1	s__UBA10364 sp013911625	78.9471	59	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445735.1	s__UBA10364 sp003445735	78.7666	103	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	97.99	97.76	0.85	0.77	3	-
GCA_905182675.1	s__UBA10364 sp905182675	77.0822	54	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:15,608] [INFO] GTDB search result was written to OceanDNA-b6025/result_gtdb.tsv
[2023-03-14 10:57:15,608] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:15,609] [INFO] DFAST_QC result json was written to OceanDNA-b6025/dqc_result.json
[2023-03-14 10:57:15,610] [INFO] DFAST_QC completed!
[2023-03-14 10:57:15,610] [INFO] Total running time: 0h1m17s