[2023-06-18 22:57:19,213] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:57:19,215] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:57:19,215] [INFO] DQC Reference Directory: /var/lib/cwl/stgea503c9b-86cb-417a-8b8a-f7471a8fb953/dqc_reference
[2023-06-18 22:57:20,507] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:57:20,508] [INFO] Task started: Prodigal
[2023-06-18 22:57:20,509] [INFO] Running command: gunzip -c /var/lib/cwl/stgaca6d5c8-da5f-42d7-8d1a-fb7df512658e/GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:57:28,279] [INFO] Task succeeded: Prodigal
[2023-06-18 22:57:28,280] [INFO] Task started: HMMsearch
[2023-06-18 22:57:28,280] [INFO] Running command: hmmsearch --tblout GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea503c9b-86cb-417a-8b8a-f7471a8fb953/dqc_reference/reference_markers.hmm GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:57:28,545] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:57:28,547] [INFO] Found 6/6 markers.
[2023-06-18 22:57:28,585] [INFO] Query marker FASTA was written to GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 22:57:28,586] [INFO] Task started: Blastn
[2023-06-18 22:57:28,586] [INFO] Running command: blastn -query GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgea503c9b-86cb-417a-8b8a-f7471a8fb953/dqc_reference/reference_markers.fasta -out GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:57:29,579] [INFO] Task succeeded: Blastn
[2023-06-18 22:57:29,583] [INFO] Selected 23 target genomes.
[2023-06-18 22:57:29,584] [INFO] Target genome list was writen to GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 22:57:29,590] [INFO] Task started: fastANI
[2023-06-18 22:57:29,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgaca6d5c8-da5f-42d7-8d1a-fb7df512658e/GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:57:47,506] [INFO] Task succeeded: fastANI
[2023-06-18 22:57:47,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea503c9b-86cb-417a-8b8a-f7471a8fb953/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:57:47,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea503c9b-86cb-417a-8b8a-f7471a8fb953/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:57:47,531] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:57:47,531] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 22:57:47,531] [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
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	80.6989	482	894	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	79.7001	438	894	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	79.6454	427	894	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	79.3684	435	894	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	79.2868	483	894	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	79.2681	413	894	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.0384	389	894	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	79.024	420	894	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	78.7134	385	894	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	78.7123	349	894	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	78.7078	383	894	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.6795	378	894	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	78.6438	355	894	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	78.6212	355	894	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	78.6046	358	894	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	78.5915	363	894	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	78.5806	362	894	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	78.5787	374	894	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.4547	382	894	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	78.3961	381	894	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	78.2969	362	894	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.196	312	894	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.1833	389	894	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 22:57:47,533] [INFO] DFAST Taxonomy check result was written to GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 22:57:47,534] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:57:47,534] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:57:47,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea503c9b-86cb-417a-8b8a-f7471a8fb953/dqc_reference/checkm_data
[2023-06-18 22:57:47,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:57:47,565] [INFO] Task started: CheckM
[2023-06-18 22:57:47,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 22:58:14,968] [INFO] Task succeeded: CheckM
[2023-06-18 22:58:14,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 22:58:14,993] [INFO] ===== Completeness check finished =====
[2023-06-18 22:58:14,993] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:58:14,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 22:58:14,994] [INFO] Task started: Blastn
[2023-06-18 22:58:14,994] [INFO] Running command: blastn -query GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgea503c9b-86cb-417a-8b8a-f7471a8fb953/dqc_reference/reference_markers_gtdb.fasta -out GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:58:16,932] [INFO] Task succeeded: Blastn
[2023-06-18 22:58:16,936] [INFO] Selected 19 target genomes.
[2023-06-18 22:58:16,936] [INFO] Target genome list was writen to GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:58:16,947] [INFO] Task started: fastANI
[2023-06-18 22:58:16,948] [INFO] Running command: fastANI --query /var/lib/cwl/stgaca6d5c8-da5f-42d7-8d1a-fb7df512658e/GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:58:30,910] [INFO] Task succeeded: fastANI
[2023-06-18 22:58:30,933] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:58:30,933] [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_001724715.1	s__SCN-67-18 sp001724715	99.9405	863	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__SCN-67-18	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004796535.1	s__Sphingomonas_L sp004796535	80.6863	483	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	79.7449	405	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034225.1	s__Sphingomonas_E fennica	79.7124	437	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	-
GCF_009913435.1	s__Sphingomonas_B sp009913435	79.6215	429	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	79.4343	328	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	79.2992	409	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	79.0604	409	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_900188165.1	s__Sphingomonas_E laterariae	79.0402	419	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050615.1	s__Sphingomonas_H oleivorans	78.992	393	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927695.1	s__Sphingomonas_K jejuensis	78.7349	347	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755815.1	s__Sphingomonas_M formosensis	78.7134	385	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789535.1	s__Sphingomonas carotinifaciens	78.5752	365	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.06	97.19	0.97	0.90	4	-
GCA_000264945.2	s__Sphingobium indicum	78.5572	375	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_002355855.1	s__Sphingobium cloacae	78.5366	366	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016025255.1	s__Allosphingosinicella sp016025255	78.3591	276	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012035195.1	s__Sphingomonas sp012035195	78.3086	397	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115745.1	s__Sphingomonas rubra	78.3017	361	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821585.1	s__UBA1936 sp013821585	78.2001	213	894	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__UBA1936	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 22:58:30,935] [INFO] GTDB search result was written to GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 22:58:30,936] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:58:30,941] [INFO] DFAST_QC result json was written to GCA_937925015.1_SRR1955887_bin.90_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 22:58:30,941] [INFO] DFAST_QC completed!
[2023-06-18 22:58:30,941] [INFO] Total running time: 0h1m12s