[2023-03-18 04:24:34,131] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:24:34,131] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:24:34,131] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c08bbb4-b9f8-4909-bded-57b98374a0f1/dqc_reference
[2023-03-18 04:24:35,782] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:24:35,782] [INFO] Task started: Prodigal
[2023-03-18 04:24:35,782] [INFO] Running command: cat /var/lib/cwl/stgf9b52d13-b803-4374-b25e-00b18b0b7c39/OceanDNA-b23103.fa | prodigal -d OceanDNA-b23103/cds.fna -a OceanDNA-b23103/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:24:59,178] [INFO] Task succeeded: Prodigal
[2023-03-18 04:24:59,178] [INFO] Task started: HMMsearch
[2023-03-18 04:24:59,178] [INFO] Running command: hmmsearch --tblout OceanDNA-b23103/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c08bbb4-b9f8-4909-bded-57b98374a0f1/dqc_reference/reference_markers.hmm OceanDNA-b23103/protein.faa > /dev/null
[2023-03-18 04:24:59,423] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:24:59,423] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf9b52d13-b803-4374-b25e-00b18b0b7c39/OceanDNA-b23103.fa]
[2023-03-18 04:24:59,462] [INFO] Query marker FASTA was written to OceanDNA-b23103/markers.fasta
[2023-03-18 04:24:59,463] [INFO] Task started: Blastn
[2023-03-18 04:24:59,463] [INFO] Running command: blastn -query OceanDNA-b23103/markers.fasta -db /var/lib/cwl/stg7c08bbb4-b9f8-4909-bded-57b98374a0f1/dqc_reference/reference_markers.fasta -out OceanDNA-b23103/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:25:00,022] [INFO] Task succeeded: Blastn
[2023-03-18 04:25:00,024] [INFO] Selected 25 target genomes.
[2023-03-18 04:25:00,024] [INFO] Target genome list was writen to OceanDNA-b23103/target_genomes.txt
[2023-03-18 04:25:00,060] [INFO] Task started: fastANI
[2023-03-18 04:25:00,061] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b52d13-b803-4374-b25e-00b18b0b7c39/OceanDNA-b23103.fa --refList OceanDNA-b23103/target_genomes.txt --output OceanDNA-b23103/fastani_result.tsv --threads 1
[2023-03-18 04:25:18,338] [INFO] Task succeeded: fastANI
[2023-03-18 04:25:18,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c08bbb4-b9f8-4909-bded-57b98374a0f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:25:18,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c08bbb4-b9f8-4909-bded-57b98374a0f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:25:18,345] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:25:18,345] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:25:18,346] [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
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.0851	57	1242	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	74.8776	85	1242	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	74.7871	79	1242	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.7585	66	1242	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	74.7137	78	1242	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	74.6272	61	1242	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	74.6147	70	1242	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	74.5578	67	1242	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	74.5534	64	1242	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	74.5278	67	1242	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:25:18,355] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23103/tc_result.tsv
[2023-03-18 04:25:18,370] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:25:18,370] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:25:18,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c08bbb4-b9f8-4909-bded-57b98374a0f1/dqc_reference/checkm_data
[2023-03-18 04:25:18,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:25:18,379] [INFO] Task started: CheckM
[2023-03-18 04:25:18,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23103/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23103/checkm_input OceanDNA-b23103/checkm_result
[2023-03-18 04:26:15,828] [INFO] Task succeeded: CheckM
[2023-03-18 04:26:15,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:26:15,919] [INFO] ===== Completeness check finished =====
[2023-03-18 04:26:15,920] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:26:15,920] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23103/markers.fasta)
[2023-03-18 04:26:15,921] [INFO] Task started: Blastn
[2023-03-18 04:26:15,921] [INFO] Running command: blastn -query OceanDNA-b23103/markers.fasta -db /var/lib/cwl/stg7c08bbb4-b9f8-4909-bded-57b98374a0f1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23103/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:26:16,688] [INFO] Task succeeded: Blastn
[2023-03-18 04:26:16,706] [INFO] Selected 23 target genomes.
[2023-03-18 04:26:16,706] [INFO] Target genome list was writen to OceanDNA-b23103/target_genomes_gtdb.txt
[2023-03-18 04:26:16,744] [INFO] Task started: fastANI
[2023-03-18 04:26:16,744] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b52d13-b803-4374-b25e-00b18b0b7c39/OceanDNA-b23103.fa --refList OceanDNA-b23103/target_genomes_gtdb.txt --output OceanDNA-b23103/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:26:34,600] [INFO] Task succeeded: fastANI
[2023-03-18 04:26:34,608] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:26:34,608] [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_017859655.1	s__JAFMMO01 sp017859655	76.3756	133	1242	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__JAFMMO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360535.1	s__F1-120-MAGs118 sp013360535	75.3861	61	1242	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525755.1	s__PLA2 sp011525755	75.1855	100	1242	d__Bacteria;p__Planctomycetota;c__PLA2;o__PLA2;f__PLA2;g__PLA2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709145.1	s__JADJEK01 sp016709145	75.0573	103	1242	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JADJEK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795255.1	s__JADJEK01 sp016795255	75.0503	82	1242	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JADJEK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716265.1	s__JADJWQ01 sp016716265	74.9716	158	1242	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JADJWQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761605.1	s__Kribbella shirazensis	74.8703	86	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235155.1	s__JACRLW01 sp016235155	74.8488	120	1242	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JACRLW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016220085.1	s__JACRIN01 sp016220085	74.8356	122	1242	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JACRIN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209535.1	s__JACQVW01 sp016209535	74.7745	104	1242	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8108;f__SXIK01;g__JACQVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297645.1	s__Dokdonella_A sp002297645	74.7597	51	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCA_016872875.1	s__DSUN01 sp016872875	74.7416	59	1242	d__Bacteria;p__Planctomycetota;c__PUPC01;o__DSUN01;f__DSUN01;g__DSUN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692555.1	s__SHYY01 sp009692555	74.6285	96	1242	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__Palsa-1104;g__SHYY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278255.1	s__Microbacterium hibisci	74.5259	67	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:26:34,620] [INFO] GTDB search result was written to OceanDNA-b23103/result_gtdb.tsv
[2023-03-18 04:26:34,638] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:26:34,648] [INFO] DFAST_QC result json was written to OceanDNA-b23103/dqc_result.json
[2023-03-18 04:26:34,648] [INFO] DFAST_QC completed!
[2023-03-18 04:26:34,649] [INFO] Total running time: 0h2m1s