[2023-03-15 07:03:38,735] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,737] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,737] [INFO] DQC Reference Directory: /var/lib/cwl/stg2980728d-dc55-4996-843b-9ab989715f38/dqc_reference
[2023-03-15 07:03:39,820] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:39,822] [INFO] Task started: Prodigal
[2023-03-15 07:03:39,822] [INFO] Running command: cat /var/lib/cwl/stg33dca4e1-29fa-4a72-bf45-4061abe87545/OceanDNA-b7881.fa | prodigal -d OceanDNA-b7881/cds.fna -a OceanDNA-b7881/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:03:47,349] [INFO] Task succeeded: Prodigal
[2023-03-15 07:03:47,349] [INFO] Task started: HMMsearch
[2023-03-15 07:03:47,349] [INFO] Running command: hmmsearch --tblout OceanDNA-b7881/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2980728d-dc55-4996-843b-9ab989715f38/dqc_reference/reference_markers.hmm OceanDNA-b7881/protein.faa > /dev/null
[2023-03-15 07:03:47,536] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:03:47,537] [INFO] Found 6/6 markers.
[2023-03-15 07:03:47,553] [INFO] Query marker FASTA was written to OceanDNA-b7881/markers.fasta
[2023-03-15 07:03:47,554] [INFO] Task started: Blastn
[2023-03-15 07:03:47,554] [INFO] Running command: blastn -query OceanDNA-b7881/markers.fasta -db /var/lib/cwl/stg2980728d-dc55-4996-843b-9ab989715f38/dqc_reference/reference_markers.fasta -out OceanDNA-b7881/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:03:48,150] [INFO] Task succeeded: Blastn
[2023-03-15 07:03:48,155] [INFO] Selected 28 target genomes.
[2023-03-15 07:03:48,155] [INFO] Target genome list was writen to OceanDNA-b7881/target_genomes.txt
[2023-03-15 07:03:48,174] [INFO] Task started: fastANI
[2023-03-15 07:03:48,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg33dca4e1-29fa-4a72-bf45-4061abe87545/OceanDNA-b7881.fa --refList OceanDNA-b7881/target_genomes.txt --output OceanDNA-b7881/fastani_result.tsv --threads 1
[2023-03-15 07:04:04,691] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:04,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2980728d-dc55-4996-843b-9ab989715f38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:04:04,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2980728d-dc55-4996-843b-9ab989715f38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:04:04,692] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:04:04,692] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:04:04,692] [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 07:04:04,696] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7881/tc_result.tsv
[2023-03-15 07:04:04,701] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:04:04,701] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:04:04,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2980728d-dc55-4996-843b-9ab989715f38/dqc_reference/checkm_data
[2023-03-15 07:04:04,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:04:04,709] [INFO] Task started: CheckM
[2023-03-15 07:04:04,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7881/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7881/checkm_input OceanDNA-b7881/checkm_result
[2023-03-15 07:04:28,960] [INFO] Task succeeded: CheckM
[2023-03-15 07:04:28,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.63%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:04:28,970] [INFO] ===== Completeness check finished =====
[2023-03-15 07:04:28,970] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:04:28,970] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7881/markers.fasta)
[2023-03-15 07:04:28,971] [INFO] Task started: Blastn
[2023-03-15 07:04:28,972] [INFO] Running command: blastn -query OceanDNA-b7881/markers.fasta -db /var/lib/cwl/stg2980728d-dc55-4996-843b-9ab989715f38/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7881/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:29,986] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:29,992] [INFO] Selected 16 target genomes.
[2023-03-15 07:04:29,992] [INFO] Target genome list was writen to OceanDNA-b7881/target_genomes_gtdb.txt
[2023-03-15 07:04:30,027] [INFO] Task started: fastANI
[2023-03-15 07:04:30,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg33dca4e1-29fa-4a72-bf45-4061abe87545/OceanDNA-b7881.fa --refList OceanDNA-b7881/target_genomes_gtdb.txt --output OceanDNA-b7881/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:04:34,881] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:34,890] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:04:34,890] [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_004214185.1	s__MAG-121220-bin8 sp004214185	96.3227	335	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.26	95.81	0.84	0.82	5	conclusive
GCA_902635895.1	s__MAG-121220-bin8 sp902635895	80.4452	191	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.57	96.57	0.70	0.70	2	-
GCA_902559035.1	s__MAG-121220-bin8 sp902559035	79.5519	244	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.40	96.04	0.82	0.79	6	-
GCA_016780345.1	s__MAG-121220-bin8 sp016780345	79.361	210	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.67	99.67	0.79	0.79	2	-
GCA_905479415.1	s__MAG-121220-bin8 sp905479415	78.2296	174	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	98.94	98.70	0.82	0.77	8	-
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	78.1681	194	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510655.1	s__MAG-121220-bin8 sp902510655	78.1273	130	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700465.1	s__MAG-121220-bin8 sp002700465	77.9927	143	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.15	98.67	0.80	0.80	3	-
GCA_018662905.1	s__MAG-121220-bin8 sp018662905	77.713	119	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.06	99.06	0.75	0.75	2	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	77.3917	117	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	77.3489	97	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	77.2204	131	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181625.1	s__MAG-121220-bin8 sp905181625	77.1706	145	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	77.0527	122	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	77.0236	133	400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:04:34,892] [INFO] GTDB search result was written to OceanDNA-b7881/result_gtdb.tsv
[2023-03-15 07:04:34,894] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:04:34,897] [INFO] DFAST_QC result json was written to OceanDNA-b7881/dqc_result.json
[2023-03-15 07:04:34,897] [INFO] DFAST_QC completed!
[2023-03-15 07:04:34,897] [INFO] Total running time: 0h0m56s