[2023-03-14 12:25:41,417] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,417] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg7324a9a1-4881-41aa-9358-e0cf0a9d9c43/dqc_reference
[2023-03-14 12:25:42,584] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,584] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,584] [INFO] Running command: cat /var/lib/cwl/stg96b462c7-7eb3-45e9-bd49-a9bad2bb9c33/OceanDNA-b21041.fa | prodigal -d OceanDNA-b21041/cds.fna -a OceanDNA-b21041/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:25:59,590] [INFO] Task succeeded: Prodigal
[2023-03-14 12:25:59,591] [INFO] Task started: HMMsearch
[2023-03-14 12:25:59,591] [INFO] Running command: hmmsearch --tblout OceanDNA-b21041/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7324a9a1-4881-41aa-9358-e0cf0a9d9c43/dqc_reference/reference_markers.hmm OceanDNA-b21041/protein.faa > /dev/null
[2023-03-14 12:25:59,787] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:25:59,788] [INFO] Found 6/6 markers.
[2023-03-14 12:25:59,812] [INFO] Query marker FASTA was written to OceanDNA-b21041/markers.fasta
[2023-03-14 12:25:59,813] [INFO] Task started: Blastn
[2023-03-14 12:25:59,813] [INFO] Running command: blastn -query OceanDNA-b21041/markers.fasta -db /var/lib/cwl/stg7324a9a1-4881-41aa-9358-e0cf0a9d9c43/dqc_reference/reference_markers.fasta -out OceanDNA-b21041/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:00,448] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:00,449] [INFO] Selected 25 target genomes.
[2023-03-14 12:26:00,449] [INFO] Target genome list was writen to OceanDNA-b21041/target_genomes.txt
[2023-03-14 12:26:00,468] [INFO] Task started: fastANI
[2023-03-14 12:26:00,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b462c7-7eb3-45e9-bd49-a9bad2bb9c33/OceanDNA-b21041.fa --refList OceanDNA-b21041/target_genomes.txt --output OceanDNA-b21041/fastani_result.tsv --threads 1
[2023-03-14 12:26:16,345] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:16,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7324a9a1-4881-41aa-9358-e0cf0a9d9c43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:26:16,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7324a9a1-4881-41aa-9358-e0cf0a9d9c43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:26:16,351] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:26:16,351] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:26:16,351] [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
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	74.9145	91	922	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	74.9012	94	922	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	74.8855	71	922	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.8125	80	922	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:26:16,351] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21041/tc_result.tsv
[2023-03-14 12:26:16,351] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:26:16,351] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:26:16,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7324a9a1-4881-41aa-9358-e0cf0a9d9c43/dqc_reference/checkm_data
[2023-03-14 12:26:16,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:26:16,511] [INFO] Task started: CheckM
[2023-03-14 12:26:16,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21041/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21041/checkm_input OceanDNA-b21041/checkm_result
[2023-03-14 12:27:00,123] [INFO] Task succeeded: CheckM
[2023-03-14 12:27:00,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.88%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:27:00,127] [INFO] ===== Completeness check finished =====
[2023-03-14 12:27:00,127] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:27:00,128] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21041/markers.fasta)
[2023-03-14 12:27:00,128] [INFO] Task started: Blastn
[2023-03-14 12:27:00,128] [INFO] Running command: blastn -query OceanDNA-b21041/markers.fasta -db /var/lib/cwl/stg7324a9a1-4881-41aa-9358-e0cf0a9d9c43/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21041/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:27:01,155] [INFO] Task succeeded: Blastn
[2023-03-14 12:27:01,155] [INFO] Selected 16 target genomes.
[2023-03-14 12:27:01,156] [INFO] Target genome list was writen to OceanDNA-b21041/target_genomes_gtdb.txt
[2023-03-14 12:27:01,170] [INFO] Task started: fastANI
[2023-03-14 12:27:01,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b462c7-7eb3-45e9-bd49-a9bad2bb9c33/OceanDNA-b21041.fa --refList OceanDNA-b21041/target_genomes_gtdb.txt --output OceanDNA-b21041/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:27:14,511] [INFO] Task succeeded: fastANI
[2023-03-14 12:27:14,519] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:27:14,519] [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_013215615.1	s__JABSQX01 sp013215615	99.3277	817	922	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQX01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013215605.1	s__JABSQW01 sp013215605	76.6064	193	922	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_004356735.1	s__SMWR01 sp004356735	76.522	89	922	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__SMWR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729515.1	s__GCA-2729515 sp002729515	76.3239	122	922	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__GCA-2729515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	76.1015	150	922	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	76.0977	134	922	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	76.0547	57	922	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_003520425.1	s__UBA9160 sp003520425	75.992	63	922	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA9160;g__UBA9160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262315.1	s__PR03 sp018262315	75.8379	90	922	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	75.7367	118	922	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_900696455.1	s__UBA2376 sp900696455	74.8139	91	922	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCA_016706545.1	s__JABFXX01 sp016706545	74.7774	63	922	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	74.7425	87	922	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707895.1	s__UBA2376 sp016707895	74.6572	108	922	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2023-03-14 12:27:14,519] [INFO] GTDB search result was written to OceanDNA-b21041/result_gtdb.tsv
[2023-03-14 12:27:14,519] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:27:14,521] [INFO] DFAST_QC result json was written to OceanDNA-b21041/dqc_result.json
[2023-03-14 12:27:14,521] [INFO] DFAST_QC completed!
[2023-03-14 12:27:14,521] [INFO] Total running time: 0h1m33s