[2023-03-19 00:15:41,732] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,732] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,732] [INFO] DQC Reference Directory: /var/lib/cwl/stga2abc8a5-1211-4dac-822a-a1417422ce2a/dqc_reference
[2023-03-19 00:15:43,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,469] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,469] [INFO] Running command: cat /var/lib/cwl/stgd2ccd4b7-9298-4781-bb8e-e5f69edadd4f/OceanDNA-b21011.fa | prodigal -d OceanDNA-b21011/cds.fna -a OceanDNA-b21011/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:16:00,051] [INFO] Task succeeded: Prodigal
[2023-03-19 00:16:00,052] [INFO] Task started: HMMsearch
[2023-03-19 00:16:00,052] [INFO] Running command: hmmsearch --tblout OceanDNA-b21011/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2abc8a5-1211-4dac-822a-a1417422ce2a/dqc_reference/reference_markers.hmm OceanDNA-b21011/protein.faa > /dev/null
[2023-03-19 00:16:00,292] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:16:00,293] [INFO] Found 6/6 markers.
[2023-03-19 00:16:00,312] [INFO] Query marker FASTA was written to OceanDNA-b21011/markers.fasta
[2023-03-19 00:16:00,313] [INFO] Task started: Blastn
[2023-03-19 00:16:00,314] [INFO] Running command: blastn -query OceanDNA-b21011/markers.fasta -db /var/lib/cwl/stga2abc8a5-1211-4dac-822a-a1417422ce2a/dqc_reference/reference_markers.fasta -out OceanDNA-b21011/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:00,921] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:00,922] [INFO] Selected 25 target genomes.
[2023-03-19 00:16:00,922] [INFO] Target genome list was writen to OceanDNA-b21011/target_genomes.txt
[2023-03-19 00:16:00,939] [INFO] Task started: fastANI
[2023-03-19 00:16:00,939] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2ccd4b7-9298-4781-bb8e-e5f69edadd4f/OceanDNA-b21011.fa --refList OceanDNA-b21011/target_genomes.txt --output OceanDNA-b21011/fastani_result.tsv --threads 1
[2023-03-19 00:16:19,041] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:19,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2abc8a5-1211-4dac-822a-a1417422ce2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:19,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2abc8a5-1211-4dac-822a-a1417422ce2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:19,047] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:19,047] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:16:19,047] [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
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1992	68	913	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.9548	56	913	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	74.8506	69	913	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	74.7785	56	913	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	74.7641	65	913	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	74.7625	76	913	95	below_threshold
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	74.7101	72	913	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:19,047] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21011/tc_result.tsv
[2023-03-19 00:16:19,048] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:19,048] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:19,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2abc8a5-1211-4dac-822a-a1417422ce2a/dqc_reference/checkm_data
[2023-03-19 00:16:19,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:19,057] [INFO] Task started: CheckM
[2023-03-19 00:16:19,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21011/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21011/checkm_input OceanDNA-b21011/checkm_result
[2023-03-19 00:17:01,651] [INFO] Task succeeded: CheckM
[2023-03-19 00:17:01,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:17:01,654] [INFO] ===== Completeness check finished =====
[2023-03-19 00:17:01,654] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:17:01,654] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21011/markers.fasta)
[2023-03-19 00:17:01,655] [INFO] Task started: Blastn
[2023-03-19 00:17:01,655] [INFO] Running command: blastn -query OceanDNA-b21011/markers.fasta -db /var/lib/cwl/stga2abc8a5-1211-4dac-822a-a1417422ce2a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21011/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:17:02,601] [INFO] Task succeeded: Blastn
[2023-03-19 00:17:02,602] [INFO] Selected 21 target genomes.
[2023-03-19 00:17:02,603] [INFO] Target genome list was writen to OceanDNA-b21011/target_genomes_gtdb.txt
[2023-03-19 00:17:02,618] [INFO] Task started: fastANI
[2023-03-19 00:17:02,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2ccd4b7-9298-4781-bb8e-e5f69edadd4f/OceanDNA-b21011.fa --refList OceanDNA-b21011/target_genomes_gtdb.txt --output OceanDNA-b21011/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:17:16,943] [INFO] Task succeeded: fastANI
[2023-03-19 00:17:16,950] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:17:16,951] [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_002687015.1	s__GCA-2687015 sp002687015	76.2597	141	913	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__GCA-2687015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262315.1	s__PR03 sp018262315	76.2044	114	913	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	76.1541	171	913	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875395.1	s__VGRF01 sp016875395	76.0646	137	913	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__VGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	75.9527	131	913	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	75.901	156	913	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	75.8984	175	913	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339255.1	s__MYXO sp905339255	75.811	80	913	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA9160;g__MYXO	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719955.1	s__UBA4427 sp002719955	75.7259	80	913	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875225.1	s__VGRW01 sp016875225	75.6687	86	913	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__VGRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220615.1	s__40CM-68-15 sp003220615	74.8887	54	913	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__40CM-68-15	95.0	99.09	97.89	0.93	0.88	5	-
GCF_002198675.1	s__R-H-3 sp002198675	74.6654	71	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:17:16,951] [INFO] GTDB search result was written to OceanDNA-b21011/result_gtdb.tsv
[2023-03-19 00:17:16,951] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:17:16,953] [INFO] DFAST_QC result json was written to OceanDNA-b21011/dqc_result.json
[2023-03-19 00:17:16,953] [INFO] DFAST_QC completed!
[2023-03-19 00:17:16,953] [INFO] Total running time: 0h1m35s