[2023-06-29 16:19:14,081] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:19:14,084] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:19:14,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg153490b5-dad3-4c53-936c-bbe756885611/dqc_reference
[2023-06-29 16:19:15,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:19:15,363] [INFO] Task started: Prodigal
[2023-06-29 16:19:15,363] [INFO] Running command: gunzip -c /var/lib/cwl/stg503b0c7b-02ea-4a03-8f3e-94849fd8066a/GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:19:26,885] [INFO] Task succeeded: Prodigal
[2023-06-29 16:19:26,885] [INFO] Task started: HMMsearch
[2023-06-29 16:19:26,885] [INFO] Running command: hmmsearch --tblout GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg153490b5-dad3-4c53-936c-bbe756885611/dqc_reference/reference_markers.hmm GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:19:27,168] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:19:27,169] [INFO] Found 6/6 markers.
[2023-06-29 16:19:27,222] [INFO] Query marker FASTA was written to GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 16:19:27,223] [INFO] Task started: Blastn
[2023-06-29 16:19:27,223] [INFO] Running command: blastn -query GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg153490b5-dad3-4c53-936c-bbe756885611/dqc_reference/reference_markers.fasta -out GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:19:28,177] [INFO] Task succeeded: Blastn
[2023-06-29 16:19:28,181] [INFO] Selected 31 target genomes.
[2023-06-29 16:19:28,181] [INFO] Target genome list was writen to GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 16:19:28,187] [INFO] Task started: fastANI
[2023-06-29 16:19:28,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg503b0c7b-02ea-4a03-8f3e-94849fd8066a/GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:19:54,110] [INFO] Task succeeded: fastANI
[2023-06-29 16:19:54,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg153490b5-dad3-4c53-936c-bbe756885611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:19:54,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg153490b5-dad3-4c53-936c-bbe756885611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:19:54,136] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:19:54,136] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:19:54,137] [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
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	77.0798	71	1125	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	76.9826	74	1125	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.8763	98	1125	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.8761	97	1125	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	76.8428	114	1125	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	76.7564	68	1125	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.7502	116	1125	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	76.73	92	1125	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	76.6278	93	1125	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	76.6244	104	1125	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	76.6138	117	1125	95	below_threshold
Pseudomonas indica	strain=JCM 21544	GCA_900100285.1	137658	137658	type	True	76.5816	102	1125	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.5085	145	1125	95	below_threshold
Halomonas ilicicola	strain=DSM 19980	GCA_900128925.1	480814	480814	type	True	76.4547	58	1125	95	below_threshold
Pseudomonas nicosulfuronedens	strain=LAM1902	GCA_005877905.1	2571105	2571105	type	True	76.436	123	1125	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	76.3827	90	1125	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.3822	113	1125	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.3766	84	1125	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	76.3498	69	1125	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	76.3407	112	1125	95	below_threshold
Pseudomonas matsuisoli	strain=JCM 30078	GCA_014647635.1	1515666	1515666	type	True	76.3296	51	1125	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	76.319	84	1125	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	76.3049	110	1125	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	76.2722	70	1125	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	76.2214	106	1125	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	76.0139	73	1125	95	below_threshold
Pseudomonas salomonii	strain=LMG 22120	GCA_001730645.1	191391	191391	type	True	76.0074	75	1125	95	below_threshold
Pseudomonas libanensis	strain=DSM 17149	GCA_001439685.1	75588	75588	type	True	75.8263	71	1125	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	75.6498	66	1125	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	75.6498	66	1125	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:19:54,139] [INFO] DFAST Taxonomy check result was written to GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 16:19:54,140] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:19:54,140] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:19:54,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg153490b5-dad3-4c53-936c-bbe756885611/dqc_reference/checkm_data
[2023-06-29 16:19:54,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:19:54,183] [INFO] Task started: CheckM
[2023-06-29 16:19:54,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 16:20:30,973] [INFO] Task succeeded: CheckM
[2023-06-29 16:20:30,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:20:30,997] [INFO] ===== Completeness check finished =====
[2023-06-29 16:20:30,997] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:20:30,998] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 16:20:30,998] [INFO] Task started: Blastn
[2023-06-29 16:20:30,998] [INFO] Running command: blastn -query GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg153490b5-dad3-4c53-936c-bbe756885611/dqc_reference/reference_markers_gtdb.fasta -out GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:20:32,556] [INFO] Task succeeded: Blastn
[2023-06-29 16:20:32,560] [INFO] Selected 30 target genomes.
[2023-06-29 16:20:32,560] [INFO] Target genome list was writen to GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:20:32,572] [INFO] Task started: fastANI
[2023-06-29 16:20:32,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg503b0c7b-02ea-4a03-8f3e-94849fd8066a/GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:20:51,915] [INFO] Task succeeded: fastANI
[2023-06-29 16:20:51,948] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:20:51,949] [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_903887045.1	s__CAILUG01 sp903887045	77.2992	205	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__CAILUG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696315.1	s__Pseudomonas_A songnenensis	76.9826	74	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	-
GCF_000341615.1	s__Pseudomonas_A stutzeri_G	76.8579	88	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.57	97.27	0.90	0.83	4	-
GCF_000364625.1	s__Pseudomonas_E thermotolerans	76.8428	114	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCA_903853385.1	s__CAILUG01 sp903853385	76.8274	144	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__CAILUG01	95.0	99.57	99.54	0.93	0.91	5	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	76.7858	67	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_001945395.1	s__Pseudomonas_E sp001945395	76.7718	103	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017589465.1	s__Pseudomonas sp017589465	76.7473	118	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837345.1	s__CAILUG01 sp903837345	76.7473	167	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__CAILUG01	95.0	99.98	99.96	1.00	0.99	3	-
GCF_000319305.2	s__Pseudomonas_E putida_C	76.73	92	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.35	97.35	0.88	0.88	2	-
GCF_005508865.1	s__Pseudomonas_E sp005508865	76.7275	127	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	76.6802	119	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	76.6436	121	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091635.1	s__Pseudomonas_M indica	76.6244	104	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	99.16	98.73	0.94	0.91	4	-
GCF_907163115.1	s__Pseudomonas_A stutzeri_AL	76.5241	105	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.05	96.55	0.94	0.91	6	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	76.5232	144	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919445.1	s__Pseudomonas sp016919445	76.4203	133	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000754225.1	s__Cobetia amphilecti	76.3693	75	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	96.77	95.09	0.91	0.86	19	-
GCF_008807415.1	s__Pseudomonas sp002079985	76.3566	144	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	97.48	95.53	0.92	0.91	9	-
GCF_016658545.1	s__Pseudomonas_E sp016658545	76.3415	86	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001945445.1	s__Pseudomonas_E sp001945445	76.2649	102	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	98.66	0.91	0.91	2	-
GCF_014297575.1	s__Dyella sp014297575	76.2471	71	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014852585.1	s__Pseudomonas sp014852585	76.2282	133	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	76.0371	77	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_016192435.1	s__Sulfuritalea sp016192435	75.9292	58	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903926285.1	s__CAILUG01 sp903926285	75.7346	68	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__CAILUG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202435.1	s__Pseudoxanthomonas broegbernensis	75.6498	66	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-29 16:20:51,951] [INFO] GTDB search result was written to GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 16:20:51,952] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:20:51,960] [INFO] DFAST_QC result json was written to GCA_937898685.1_SRR4028131_bin.63_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 16:20:51,961] [INFO] DFAST_QC completed!
[2023-06-29 16:20:51,961] [INFO] Total running time: 0h1m38s