[2023-03-15 23:42:29,662] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:42:29,662] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:42:29,662] [INFO] DQC Reference Directory: /var/lib/cwl/stgd75c00b4-2613-4c6e-b216-5fbf848d2cdb/dqc_reference
[2023-03-15 23:42:31,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:42:31,276] [INFO] Task started: Prodigal
[2023-03-15 23:42:31,276] [INFO] Running command: cat /var/lib/cwl/stg5aba043a-0060-423f-ac3f-ec019c2c614a/OceanDNA-b8989.fa | prodigal -d OceanDNA-b8989/cds.fna -a OceanDNA-b8989/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:42:42,142] [INFO] Task succeeded: Prodigal
[2023-03-15 23:42:42,143] [INFO] Task started: HMMsearch
[2023-03-15 23:42:42,143] [INFO] Running command: hmmsearch --tblout OceanDNA-b8989/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd75c00b4-2613-4c6e-b216-5fbf848d2cdb/dqc_reference/reference_markers.hmm OceanDNA-b8989/protein.faa > /dev/null
[2023-03-15 23:42:42,336] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:42:42,337] [INFO] Found 6/6 markers.
[2023-03-15 23:42:42,349] [INFO] Query marker FASTA was written to OceanDNA-b8989/markers.fasta
[2023-03-15 23:42:42,351] [INFO] Task started: Blastn
[2023-03-15 23:42:42,351] [INFO] Running command: blastn -query OceanDNA-b8989/markers.fasta -db /var/lib/cwl/stgd75c00b4-2613-4c6e-b216-5fbf848d2cdb/dqc_reference/reference_markers.fasta -out OceanDNA-b8989/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:42:42,884] [INFO] Task succeeded: Blastn
[2023-03-15 23:42:42,884] [INFO] Selected 29 target genomes.
[2023-03-15 23:42:42,885] [INFO] Target genome list was writen to OceanDNA-b8989/target_genomes.txt
[2023-03-15 23:42:42,904] [INFO] Task started: fastANI
[2023-03-15 23:42:42,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg5aba043a-0060-423f-ac3f-ec019c2c614a/OceanDNA-b8989.fa --refList OceanDNA-b8989/target_genomes.txt --output OceanDNA-b8989/fastani_result.tsv --threads 1
[2023-03-15 23:42:59,906] [INFO] Task succeeded: fastANI
[2023-03-15 23:42:59,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd75c00b4-2613-4c6e-b216-5fbf848d2cdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:42:59,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd75c00b4-2613-4c6e-b216-5fbf848d2cdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:42:59,907] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:42:59,907] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:42:59,907] [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 23:42:59,907] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8989/tc_result.tsv
[2023-03-15 23:42:59,907] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:42:59,907] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:42:59,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd75c00b4-2613-4c6e-b216-5fbf848d2cdb/dqc_reference/checkm_data
[2023-03-15 23:42:59,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:42:59,913] [INFO] Task started: CheckM
[2023-03-15 23:42:59,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8989/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8989/checkm_input OceanDNA-b8989/checkm_result
[2023-03-15 23:43:30,659] [INFO] Task succeeded: CheckM
[2023-03-15 23:43:30,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:43:30,661] [INFO] ===== Completeness check finished =====
[2023-03-15 23:43:30,662] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:43:30,662] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8989/markers.fasta)
[2023-03-15 23:43:30,663] [INFO] Task started: Blastn
[2023-03-15 23:43:30,663] [INFO] Running command: blastn -query OceanDNA-b8989/markers.fasta -db /var/lib/cwl/stgd75c00b4-2613-4c6e-b216-5fbf848d2cdb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8989/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:43:31,462] [INFO] Task succeeded: Blastn
[2023-03-15 23:43:31,463] [INFO] Selected 26 target genomes.
[2023-03-15 23:43:31,463] [INFO] Target genome list was writen to OceanDNA-b8989/target_genomes_gtdb.txt
[2023-03-15 23:43:31,531] [INFO] Task started: fastANI
[2023-03-15 23:43:31,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg5aba043a-0060-423f-ac3f-ec019c2c614a/OceanDNA-b8989.fa --refList OceanDNA-b8989/target_genomes_gtdb.txt --output OceanDNA-b8989/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:43:39,238] [INFO] Task succeeded: fastANI
[2023-03-15 23:43:39,251] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:43:39,251] [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_902616905.1	s__MS024-2A sp902616905	88.5693	378	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525195.1	s__MS024-2A sp011525195	77.361	82	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902613595.1	s__MS024-2A sp902613595	77.3522	161	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003130815.1	s__MS024-2A sp003130815	77.3519	149	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714815.1	s__MS024-2A sp002714815	77.3148	187	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618245.1	s__MS024-2A sp902618245	77.3111	157	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.05	96.19	0.87	0.86	3	-
GCA_902561795.1	s__MS024-2A sp902561795	77.0915	142	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517245.1	s__MS024-2A sp902517245	77.0089	127	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512755.1	s__MS024-2A sp902512755	76.7974	94	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546725.1	s__MS024-2A sp902546725	76.7948	67	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000173095.1	s__MS024-2A sp000173095	76.683	88	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	-
GCA_002292265.1	s__MS024-2A sp002292265	76.5716	92	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.71	99.21	0.94	0.92	6	-
GCA_017852075.1	s__MS024-2A sp017852075	76.5418	95	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
GCA_002167945.1	s__MS024-2A sp002167945	76.5343	81	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886625.1	s__MS024-2A sp009886625	76.333	98	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690805.1	s__GCA-002723295 sp002690805	76.3222	65	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	97.07	97.07	0.76	0.76	2	-
GCA_905182735.1	s__GCA-002723295 sp905182735	76.2979	75	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017851655.1	s__MS024-2A sp017851655	76.2274	90	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.55	99.53	0.87	0.86	3	-
GCA_017858055.1	s__MS024-2A sp002384715	76.2072	71	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.54	99.54	0.94	0.94	2	-
GCA_905181895.1	s__MS024-2A sp905181895	76.0176	69	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719315.1	s__GCA-2719315 sp002719315	75.94	92	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902598305.1	s__TMED96 sp902598305	75.8412	52	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905381055.1	s__TMED220 sp905381055	75.7214	67	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:43:39,252] [INFO] GTDB search result was written to OceanDNA-b8989/result_gtdb.tsv
[2023-03-15 23:43:39,252] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:43:39,253] [INFO] DFAST_QC result json was written to OceanDNA-b8989/dqc_result.json
[2023-03-15 23:43:39,253] [INFO] DFAST_QC completed!
[2023-03-15 23:43:39,253] [INFO] Total running time: 0h1m10s