[2023-03-15 03:02:04,675] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:02:04,675] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:02:04,675] [INFO] DQC Reference Directory: /var/lib/cwl/stg719ad0b3-8f20-4d9a-bd99-7ccad134d60a/dqc_reference
[2023-03-15 03:02:05,816] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:02:05,817] [INFO] Task started: Prodigal
[2023-03-15 03:02:05,818] [INFO] Running command: cat /var/lib/cwl/stgf2a608da-3af6-48e0-8c59-efb3e78981a9/OceanDNA-b41055.fa | prodigal -d OceanDNA-b41055/cds.fna -a OceanDNA-b41055/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:02:30,745] [INFO] Task succeeded: Prodigal
[2023-03-15 03:02:30,745] [INFO] Task started: HMMsearch
[2023-03-15 03:02:30,745] [INFO] Running command: hmmsearch --tblout OceanDNA-b41055/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg719ad0b3-8f20-4d9a-bd99-7ccad134d60a/dqc_reference/reference_markers.hmm OceanDNA-b41055/protein.faa > /dev/null
[2023-03-15 03:02:30,952] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:02:30,952] [INFO] Found 6/6 markers.
[2023-03-15 03:02:30,975] [INFO] Query marker FASTA was written to OceanDNA-b41055/markers.fasta
[2023-03-15 03:02:30,977] [INFO] Task started: Blastn
[2023-03-15 03:02:30,977] [INFO] Running command: blastn -query OceanDNA-b41055/markers.fasta -db /var/lib/cwl/stg719ad0b3-8f20-4d9a-bd99-7ccad134d60a/dqc_reference/reference_markers.fasta -out OceanDNA-b41055/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:02:31,853] [INFO] Task succeeded: Blastn
[2023-03-15 03:02:31,854] [INFO] Selected 17 target genomes.
[2023-03-15 03:02:31,854] [INFO] Target genome list was writen to OceanDNA-b41055/target_genomes.txt
[2023-03-15 03:02:31,862] [INFO] Task started: fastANI
[2023-03-15 03:02:31,862] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2a608da-3af6-48e0-8c59-efb3e78981a9/OceanDNA-b41055.fa --refList OceanDNA-b41055/target_genomes.txt --output OceanDNA-b41055/fastani_result.tsv --threads 1
[2023-03-15 03:02:43,395] [INFO] Task succeeded: fastANI
[2023-03-15 03:02:43,395] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg719ad0b3-8f20-4d9a-bd99-7ccad134d60a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:02:43,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg719ad0b3-8f20-4d9a-bd99-7ccad134d60a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:02:43,412] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:02:43,413] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:02:43,413] [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
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	79.6115	510	1338	95	below_threshold
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	79.5969	514	1338	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	79.4046	436	1338	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	79.314	439	1338	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	79.278	432	1338	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	79.1976	406	1338	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	79.0615	395	1338	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	78.9672	436	1338	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	78.8909	447	1338	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	78.0239	266	1338	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.8405	302	1338	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	77.74	258	1338	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	77.6987	254	1338	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	77.649	264	1338	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	77.5552	248	1338	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.5493	283	1338	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	77.2883	247	1338	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:02:43,413] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41055/tc_result.tsv
[2023-03-15 03:02:43,413] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:02:43,413] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:02:43,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg719ad0b3-8f20-4d9a-bd99-7ccad134d60a/dqc_reference/checkm_data
[2023-03-15 03:02:43,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:02:43,419] [INFO] Task started: CheckM
[2023-03-15 03:02:43,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41055/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41055/checkm_input OceanDNA-b41055/checkm_result
[2023-03-15 03:03:46,761] [INFO] Task succeeded: CheckM
[2023-03-15 03:03:46,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:03:46,764] [INFO] ===== Completeness check finished =====
[2023-03-15 03:03:46,764] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:03:46,764] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41055/markers.fasta)
[2023-03-15 03:03:46,766] [INFO] Task started: Blastn
[2023-03-15 03:03:46,766] [INFO] Running command: blastn -query OceanDNA-b41055/markers.fasta -db /var/lib/cwl/stg719ad0b3-8f20-4d9a-bd99-7ccad134d60a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41055/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:03:48,394] [INFO] Task succeeded: Blastn
[2023-03-15 03:03:48,395] [INFO] Selected 11 target genomes.
[2023-03-15 03:03:48,395] [INFO] Target genome list was writen to OceanDNA-b41055/target_genomes_gtdb.txt
[2023-03-15 03:03:48,404] [INFO] Task started: fastANI
[2023-03-15 03:03:48,405] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2a608da-3af6-48e0-8c59-efb3e78981a9/OceanDNA-b41055.fa --refList OceanDNA-b41055/target_genomes_gtdb.txt --output OceanDNA-b41055/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:03:56,590] [INFO] Task succeeded: fastANI
[2023-03-15 03:03:56,597] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:03:56,597] [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_009497895.1	s__Pseudomonas_D pelagia_A	83.8542	920	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365385.1	s__Pseudomonas_D laoshanensis	83.6494	869	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
GCF_000410875.1	s__Pseudomonas_D pelagia	82.6585	845	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840055.1	s__Pseudomonas_D sp002840055	80.0272	409	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008641105.1	s__Pseudomonas_D salina	79.6143	512	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016763285.1	s__Pseudomonas_D sp016763285	79.1328	418	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008638305.1	s__Pseudomonas_D profundi	79.07	393	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.49	98.49	0.91	0.91	2	-
GCF_000939975.1	s__Pseudomonas_D saudimassiliensis	79.0657	432	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105255.1	s__Pseudomonas_D sabulinigri	79.0476	486	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115905.1	s__Pseudomonas_D formosensis	78.7795	395	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.74	98.74	0.94	0.94	2	-
GCA_011053055.1	s__Pseudomonas_D sabulinigri_A	78.1893	344	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.96	99.96	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-15 03:03:56,598] [INFO] GTDB search result was written to OceanDNA-b41055/result_gtdb.tsv
[2023-03-15 03:03:56,598] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:03:56,599] [INFO] DFAST_QC result json was written to OceanDNA-b41055/dqc_result.json
[2023-03-15 03:03:56,599] [INFO] DFAST_QC completed!
[2023-03-15 03:03:56,599] [INFO] Total running time: 0h1m52s