[2023-03-15 04:37:12,255] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:37:12,264] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:37:12,264] [INFO] DQC Reference Directory: /var/lib/cwl/stgb556f4be-08ed-4883-b96d-706aa41b1dd7/dqc_reference
[2023-03-15 04:37:13,359] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:37:13,359] [INFO] Task started: Prodigal
[2023-03-15 04:37:13,359] [INFO] Running command: cat /var/lib/cwl/stg8cc989be-6bc1-4c21-ac4c-6d807fd0d0cb/OceanDNA-b13096.fa | prodigal -d OceanDNA-b13096/cds.fna -a OceanDNA-b13096/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:37:49,939] [INFO] Task succeeded: Prodigal
[2023-03-15 04:37:49,939] [INFO] Task started: HMMsearch
[2023-03-15 04:37:49,939] [INFO] Running command: hmmsearch --tblout OceanDNA-b13096/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb556f4be-08ed-4883-b96d-706aa41b1dd7/dqc_reference/reference_markers.hmm OceanDNA-b13096/protein.faa > /dev/null
[2023-03-15 04:37:50,163] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:37:50,164] [INFO] Found 6/6 markers.
[2023-03-15 04:37:50,265] [INFO] Query marker FASTA was written to OceanDNA-b13096/markers.fasta
[2023-03-15 04:37:50,266] [INFO] Task started: Blastn
[2023-03-15 04:37:50,266] [INFO] Running command: blastn -query OceanDNA-b13096/markers.fasta -db /var/lib/cwl/stgb556f4be-08ed-4883-b96d-706aa41b1dd7/dqc_reference/reference_markers.fasta -out OceanDNA-b13096/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:37:50,953] [INFO] Task succeeded: Blastn
[2023-03-15 04:37:50,975] [INFO] Selected 18 target genomes.
[2023-03-15 04:37:50,976] [INFO] Target genome list was writen to OceanDNA-b13096/target_genomes.txt
[2023-03-15 04:37:50,987] [INFO] Task started: fastANI
[2023-03-15 04:37:50,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cc989be-6bc1-4c21-ac4c-6d807fd0d0cb/OceanDNA-b13096.fa --refList OceanDNA-b13096/target_genomes.txt --output OceanDNA-b13096/fastani_result.tsv --threads 1
[2023-03-15 04:38:06,856] [INFO] Task succeeded: fastANI
[2023-03-15 04:38:06,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb556f4be-08ed-4883-b96d-706aa41b1dd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:38:06,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb556f4be-08ed-4883-b96d-706aa41b1dd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:38:06,866] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:38:06,866] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:38:06,866] [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
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	82.0447	1013	1520	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	78.87	556	1520	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.7286	226	1520	95	below_threshold
Longibacter salinarum	strain=KCTC 52045	GCA_002554795.1	1850348	1850348	type	True	76.0734	60	1520	95	below_threshold
Salinibacter altiplanensis	strain=AN15	GCA_002894645.1	1803181	1803181	type	True	75.8035	84	1520	95	below_threshold
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	75.7818	102	1520	95	below_threshold
Salisaeta longa	strain=DSM 21114	GCA_000419585.1	503170	503170	type	True	75.7167	87	1520	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	75.012	137	1520	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	74.9798	207	1520	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.9592	296	1520	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	74.9285	180	1520	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	74.9158	184	1520	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	74.9071	205	1520	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	74.8771	156	1520	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.8732	265	1520	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:38:06,874] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13096/tc_result.tsv
[2023-03-15 04:38:06,888] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:38:06,888] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:38:06,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb556f4be-08ed-4883-b96d-706aa41b1dd7/dqc_reference/checkm_data
[2023-03-15 04:38:06,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:38:06,897] [INFO] Task started: CheckM
[2023-03-15 04:38:06,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13096/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13096/checkm_input OceanDNA-b13096/checkm_result
[2023-03-15 04:39:33,833] [INFO] Task succeeded: CheckM
[2023-03-15 04:39:33,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:39:33,844] [INFO] ===== Completeness check finished =====
[2023-03-15 04:39:33,844] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:39:33,844] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13096/markers.fasta)
[2023-03-15 04:39:33,845] [INFO] Task started: Blastn
[2023-03-15 04:39:33,845] [INFO] Running command: blastn -query OceanDNA-b13096/markers.fasta -db /var/lib/cwl/stgb556f4be-08ed-4883-b96d-706aa41b1dd7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13096/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:39:35,034] [INFO] Task succeeded: Blastn
[2023-03-15 04:39:35,036] [INFO] Selected 8 target genomes.
[2023-03-15 04:39:35,036] [INFO] Target genome list was writen to OceanDNA-b13096/target_genomes_gtdb.txt
[2023-03-15 04:39:35,044] [INFO] Task started: fastANI
[2023-03-15 04:39:35,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cc989be-6bc1-4c21-ac4c-6d807fd0d0cb/OceanDNA-b13096.fa --refList OceanDNA-b13096/target_genomes_gtdb.txt --output OceanDNA-b13096/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:39:42,920] [INFO] Task succeeded: fastANI
[2023-03-15 04:39:42,925] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:39:42,925] [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
GCF_002283555.1	s__Rubrivirga sp002283555	98.4242	1361	1520	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	conclusive
GCF_002283365.1	s__Rubrivirga marina	82.0758	1009	1520	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269805.1	s__Rubrivirga sp012269805	81.75	636	1520	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960515.1	s__Rubricoccus sp012960515	80.1795	562	1520	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257665.1	s__Rubricoccus marinus	78.8401	562	1520	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003465.1	s__JABDIZ01 sp013003465	77.9139	280	1520	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__JABDIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908885.1	s__JAAAOL01 sp009908885	76.7259	217	1520	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__JAAAOL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001788415.1	s__UBA12499 sp001788415	74.9385	109	1520	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__UBA12499	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:39:42,926] [INFO] GTDB search result was written to OceanDNA-b13096/result_gtdb.tsv
[2023-03-15 04:39:42,927] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:39:42,928] [INFO] DFAST_QC result json was written to OceanDNA-b13096/dqc_result.json
[2023-03-15 04:39:42,928] [INFO] DFAST_QC completed!
[2023-03-15 04:39:42,928] [INFO] Total running time: 0h2m31s