[2023-03-15 07:03:38,797] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,797] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg681f9cdf-d3a3-449c-bea1-fd38d5aa63d1/dqc_reference
[2023-03-15 07:03:39,985] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:39,986] [INFO] Task started: Prodigal
[2023-03-15 07:03:39,986] [INFO] Running command: cat /var/lib/cwl/stg497f6ed0-b89d-43d4-b53d-5cb200736eaf/OceanDNA-b5007.fa | prodigal -d OceanDNA-b5007/cds.fna -a OceanDNA-b5007/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:03:48,057] [INFO] Task succeeded: Prodigal
[2023-03-15 07:03:48,057] [INFO] Task started: HMMsearch
[2023-03-15 07:03:48,057] [INFO] Running command: hmmsearch --tblout OceanDNA-b5007/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg681f9cdf-d3a3-449c-bea1-fd38d5aa63d1/dqc_reference/reference_markers.hmm OceanDNA-b5007/protein.faa > /dev/null
[2023-03-15 07:03:48,226] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:03:48,227] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg497f6ed0-b89d-43d4-b53d-5cb200736eaf/OceanDNA-b5007.fa]
[2023-03-15 07:03:48,246] [INFO] Query marker FASTA was written to OceanDNA-b5007/markers.fasta
[2023-03-15 07:03:48,247] [INFO] Task started: Blastn
[2023-03-15 07:03:48,247] [INFO] Running command: blastn -query OceanDNA-b5007/markers.fasta -db /var/lib/cwl/stg681f9cdf-d3a3-449c-bea1-fd38d5aa63d1/dqc_reference/reference_markers.fasta -out OceanDNA-b5007/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:03:48,818] [INFO] Task succeeded: Blastn
[2023-03-15 07:03:48,824] [INFO] Selected 23 target genomes.
[2023-03-15 07:03:48,824] [INFO] Target genome list was writen to OceanDNA-b5007/target_genomes.txt
[2023-03-15 07:03:48,860] [INFO] Task started: fastANI
[2023-03-15 07:03:48,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg497f6ed0-b89d-43d4-b53d-5cb200736eaf/OceanDNA-b5007.fa --refList OceanDNA-b5007/target_genomes.txt --output OceanDNA-b5007/fastani_result.tsv --threads 1
[2023-03-15 07:04:00,938] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:00,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg681f9cdf-d3a3-449c-bea1-fd38d5aa63d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:04:00,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg681f9cdf-d3a3-449c-bea1-fd38d5aa63d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:04:00,939] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:04:00,939] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:04:00,939] [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
--------------------------------------------------------------------------------
[2023-03-15 07:04:00,943] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5007/tc_result.tsv
[2023-03-15 07:04:00,949] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:04:00,949] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:04:00,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg681f9cdf-d3a3-449c-bea1-fd38d5aa63d1/dqc_reference/checkm_data
[2023-03-15 07:04:00,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:04:00,964] [INFO] Task started: CheckM
[2023-03-15 07:04:00,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5007/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5007/checkm_input OceanDNA-b5007/checkm_result
[2023-03-15 07:04:26,563] [INFO] Task succeeded: CheckM
[2023-03-15 07:04:26,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:04:26,575] [INFO] ===== Completeness check finished =====
[2023-03-15 07:04:26,576] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:04:26,576] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5007/markers.fasta)
[2023-03-15 07:04:26,577] [INFO] Task started: Blastn
[2023-03-15 07:04:26,577] [INFO] Running command: blastn -query OceanDNA-b5007/markers.fasta -db /var/lib/cwl/stg681f9cdf-d3a3-449c-bea1-fd38d5aa63d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5007/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:27,519] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:27,535] [INFO] Selected 26 target genomes.
[2023-03-15 07:04:27,535] [INFO] Target genome list was writen to OceanDNA-b5007/target_genomes_gtdb.txt
[2023-03-15 07:04:27,626] [INFO] Task started: fastANI
[2023-03-15 07:04:27,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg497f6ed0-b89d-43d4-b53d-5cb200736eaf/OceanDNA-b5007.fa --refList OceanDNA-b5007/target_genomes_gtdb.txt --output OceanDNA-b5007/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:04:35,030] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:35,038] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:04:35,038] [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_002715885.1	s__GCA-002715885 sp002715885	95.1179	257	438	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902579065.1	s__GCA-002715885 sp902579065	79.1757	165	438	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239655.1	s__GCA-002715885 sp014239655	77.2862	139	438	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689735.1	s__GCA-002715885 sp002689735	77.2167	102	438	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	96.30	96.30	0.76	0.76	2	-
GCA_018675825.1	s__GCA-002715885 sp018675825	76.7263	99	438	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478555.1	s__GCA-002697625 sp905478555	76.4072	50	438	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	96.63	96.63	0.87	0.87	2	-
GCA_002711125.1	s__GCA-2711125 sp002711125	76.3917	75	438	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	97.93	96.61	0.96	0.94	3	-
GCA_002728175.1	s__GCA-2697505 sp002728175	76.2507	83	438	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724895.1	s__GCA-2693335 sp002724895	76.2201	71	438	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2693335	95.0	97.78	97.48	0.81	0.76	3	-
GCA_902587125.1	s__GCA-2716345 sp902587125	75.8987	51	438	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2716345	95.0	98.85	98.45	0.91	0.90	4	-
GCA_905478185.1	s__UWMA-0277 sp905478185	75.7423	54	438	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-15 07:04:35,040] [INFO] GTDB search result was written to OceanDNA-b5007/result_gtdb.tsv
[2023-03-15 07:04:35,041] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:04:35,043] [INFO] DFAST_QC result json was written to OceanDNA-b5007/dqc_result.json
[2023-03-15 07:04:35,044] [INFO] DFAST_QC completed!
[2023-03-15 07:04:35,044] [INFO] Total running time: 0h0m56s